Add USE_FC_LEN_T to satisfy CRAN

- This concerns a change to R 3.6.5 which will be required in R 4.2.0

- has something to do with passing character strings from C to Fortran,
  used in effectscan.c and lapackutil.c. (Was able to just delete
  one function from lapackutil.c.)

- See <https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Fortran-character-strings>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qtl
-Version: 1.49-2
-Date: 2021-08-05
+Version: 1.49-3
+Date: 2021-09-25
 Title: Tools for Analyzing QTL Experiments
 Author: Karl W Broman <[email protected]> and Hao Wu, with
   ideas from Gary Churchill and Saunak Sen and contributions from

NEWS.md

@@ -27,6 +27,9 @@ copyright (c) 2001-2021, Karl W Broman
 
 - Revised qtlversion() to handle a case like "1.50".
 
+- Added `#define USE_FC_LEN_T` in C code that calls Fortran, because
+  of a change in R 3.6.5 that's going to be required in R 4.2.0.
+
 
 ## Version 1.48, 2021-03-24
 

src/effectscan.c

@@ -2,9 +2,9 @@
  *
  * effectscan.c
  *
- * copyright (c) 2007-8, Karl W Broman
+ * copyright (c) 2007-2021, Karl W Broman
  *
- * last modified Jan, 2008
+ * last modified Sep, 2021
  * first written Sep, 2007
  *
  *     This program is free software; you can redistribute it and/or
@@ -28,16 +28,21 @@
  *
  **********************************************************************/
 
+#define USE_FC_LEN_T
 #include <math.h>
 #include <stdlib.h>
 #include <stdio.h>
+#include <Rconfig.h>
 #include <R.h>
 #include <Rmath.h>
 #include <R_ext/PrtUtil.h>
 #include <R_ext/Applic.h>
 #include <R_ext/Lapack.h>
 #include "effectscan.h"
 #include "util.h"
+#ifndef FCONE
+# define FCONE
+#endif
 
 /* R_effectscan: wrapper for effectscan */
 
@@ -126,7 +131,7 @@ void effectscan(int nind, int ngen, int ndraws, int npos,
             if(!flag[i]) {
                 /* linear regression */
                 F77_CALL(dgels)("N", &nind, &ngen, &nphe, x, &nind, resid, &nind,
-                                dwork, &lwork, &info);
+                                dwork, &lwork, &info FCONE);
 
                 /* coefficient estimates */
                 for(j=0; j<ngen; j++) wbeta[j+i*ngen] = resid[j];
@@ -147,7 +152,7 @@ void effectscan(int nind, int ngen, int ndraws, int npos,
                     memcpy(var+j*ngen, x+j*nind, ngen*sizeof(double));
 
                 /* (X'X)^-1 */
-                F77_CALL(dpotri)("U", &ngen, var, &ngen, &info);
+                F77_CALL(dpotri)("U", &ngen, var, &ngen, &info FCONE);
 
                 /* estimated variances of estimated coefficients */
                 for(j=0; j<ngen; j++) wvar[j + i*ngen] = sigmasq * var[j+j*ngen];

src/lapackutil.c

@@ -2,9 +2,9 @@
  *
  * lapackutil.c
  *
- * copyright (c) 2006, Hao Wu
+ * copyright (c) 2006-2021, Hao Wu and Karl Broman
  *
- * last modified Feb, 2006
+ * last modified Sep, 2021
  * first written Jan, 2006
  *
  *     This program is free software; you can redistribute it and/or
@@ -27,16 +27,21 @@
  *
  **********************************************************************/
 
+#define USE_FC_LEN_T
 #include <math.h>
 #include <stdlib.h>
 #include <stdio.h>
+#include <Rconfig.h>
 #include <R.h>
 #include <Rmath.h>
 #include <R_ext/PrtUtil.h>
 #include <R_ext/Applic.h>
 #include <R_ext/Lapack.h>
 #include "lapackutil.h"
 #define TOL 1e-12
+#ifndef FCONE
+# define FCONE
+#endif
 
 
 /* DGELSS function */
@@ -48,7 +53,7 @@ void mydgelss (int *n_ind, int *ncolx0, int *nphe, double *x0, double *x0_bk,
 
     /* use dgels first */
     F77_CALL(dgels)("N", n_ind, ncolx0, nphe, x0, n_ind, tmppheno, n_ind,
-                    work, lwork, info);
+                    work, lwork, info FCONE);
 
     /* if there's problem like singular, use dgelss */
     /* note that x0 will contain the result for QR decomposition.
@@ -81,21 +86,15 @@ void mydgemm(int *nphe, int *n_ind, double *alpha, double *tmppheno,
              double *beta, double *rss_det)
 {
     F77_CALL(dgemm)("T", "N", nphe, nphe, n_ind, alpha, tmppheno, n_ind,
-                    tmppheno, n_ind, beta, rss_det, nphe);
+                    tmppheno, n_ind, beta, rss_det, nphe FCONE FCONE);
 }
 
 /* DPOTRF */
 void mydpotrf(int *nphe, double *rss_det, int *info)
 {
-    F77_CALL(dpotrf)("U", nphe, rss_det, nphe, info);
+    F77_CALL(dpotrf)("U", nphe, rss_det, nphe, info FCONE);
 }
 
-/*DPOTRS */
-void mydpotrs(char *uplo, int *n, int *nrhs, double *A,
-              int *lda, double *B, int *ldb, int *info)
-{
-    F77_CALL(dpotrs)(uplo, n, nrhs, A, lda, B, ldb, info);
-}
 
 
 /* end of lapackutil.c */

src/lapackutil.h

@@ -23,7 +23,7 @@
  *
  * These are some wrapper functions for several LAPACK routines.
  *
- * Contains: mydgelss, mydgemm, mydpotrf, mydpotrs
+ * Contains: mydgelss, mydgemm, mydpotrf
  *
  **********************************************************************/
 
@@ -39,8 +39,4 @@ void mydgemm(int *nphe, int *n_ind, double *alpha, double *tmppheno, double *bet
 /* DPOTRF */
 void mydpotrf(int *nphe1, double *rss_det, int *info);
 
-/* DPOTRS */
-void mydpotrs(char *uplo, int *n, int *nrhs, double *A,
-              int *lda, double *B, int *ldb, int *info);
-
 /* end of lapackutil.h */

src/util.c

@@ -41,7 +41,6 @@
  **********************************************************************/
 
 #include <R.h>
-/* #include <R_ext/BLAS.h> */
 #include "util.h"
 
 #define THRESH 200.0
@@ -702,17 +701,6 @@ void locate_xo(int n_ind, int n_mar, int type, int **Geno,
     } /* end loop over individuals */
 }
 
-/* multiply two matrices - I'm using dgemm from lapack here */
-/*
-  void matmult2(double *result, double *a, int nrowa,
-  int ncola, double *b, int ncolb)
-
-  {
-  double alpha=1.0, beta=1.0;
-  F77_CALL(dgemm)("N", "N", &nrowa, &ncolb, &ncola, &alpha, a, &nrowa,
-  b, &ncola, &beta, result, &nrowa);
-  }
-*/
 
 void matmult(double *result, double *a, int nrowa,
              int ncola, double *b, int ncolb)