debugged noLD uniroot tolerance issue

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: bnpsd
 Title: Simulate Genotypes from the BN-PSD Admixture Model
-Version: 1.2.0
+Version: 1.2.1
 Authors@R: c(
     person(given = "Alejandro",
 	   family = "Ochoa",

NEWS.md

@@ -111,3 +111,11 @@ These loci are not polymorphic so they would normally not be considered in analy
 * Removed deprecated function names: `q1dc`, `q1d`, `qis`, `coanc`, `rbnpsd`, `rgeno`, `rpanc`, `rpint`, `rpiaf`.
 * Moved logo to `man/figures/`
 * Minor Roxygen-related updates.
+
+# 2020-01-08 - bnpsd 1.2.1
+
+* Fourth CRAN submission, second attempt.
+* Fixed a rare bug in `bias_coeff_admix_fit`, which caused it to die if the desired bias coefficient was an extreme value (particularly `1`).
+  The error message was: `f() values at end points not of opposite sign`.
+  The actual bug was not observed in the regular R build, but rather in a limited precision setting where R was configured with `--disable-long-double`.
+

R/bias_coeff_admix_fit.R

@@ -72,6 +72,12 @@ bias_coeff_admix_fit <- function(
     bias_coeff_min <- bias_coeff_admix(admix_prop_bias_coeff_min, coanc_subpops)
     if (bias_coeff < bias_coeff_min)
         stop('Desired `bias_coeff` must be greater than ', bias_coeff_min, ' (the minimum achievable with `sigma = 0`), passed ', bias_coeff)
+
+    # tolerance should be precision-dependent, but when configured with --disable-long-double the value of .Machine$double.eps doesn't change!
+    # so here we test for that config difference (by testing if .Machine$sizeof.longdouble is zero) and reduce the tolerance accordingly
+    tol <- .Machine$double.eps
+    if ( .Machine$sizeof.longdouble == 0 )
+        tol <- sqrt( tol )
 
     # function whose zero we want!
     # "sigma" is the only parameter to optimize
@@ -90,15 +96,23 @@ bias_coeff_admix_fit <- function(
             coord_ind_last = coord_ind_last
         )
         # get bias coefficient, return difference from desired value!
-        bias_coeff_admix(admix_proportions, coanc_subpops) - bias_coeff
+        delta <- bias_coeff_admix(admix_proportions, coanc_subpops) - bias_coeff
+
+        # hack to prevent issues when attempting to fit extreme values (at boundaries)
+        # in particular, without this (and in particular in lower precision settings, such as --disable-long-double), uniroot below complains because delta has the same sign on both extrema (due to machine error, not a real sign issue).  If the sign wasn't checked then the tolerance would find that the solution is at the boundary, so here we force the check earlier.
+        if ( abs(delta) < tol )
+            delta <- 0
+
+        # return delta now
+        return( delta )
     }
 
     # default tolerance of .Machine$double.eps^0.25 (~ 1e-4) was not good enough, reduced to ~ 2e-16
     obj <- stats::uniroot(
                       bias_coeff_admix_objective,
                       interval = c(0, 1),
                       extendInt = "no",
-                      tol = .Machine$double.eps
+                      tol = tol
                   )
     # this is the value in terms of `x`
     x_root <- obj$root

cran-comments.md

@@ -1,8 +1,10 @@
 ## Test environments
-* local: x86_64-redhat-linux-gnu R 3.6.2
-* win-builder devel: x86_64-w64-mingw32 R Under development (unstable) (2020-01-03 r77630)
-* win-builder release: x86_64-w64-mingw32 R 3.6.2 (2019-12-12)
-* rhub: (debian) x86_64-pc-linux-gnu R Under development (unstable) (2020-01-03 r77629)
+* local R:             x86_64-redhat-linux-gnu R 3.6.2
+* local R-devel:       x86_64-redhat-linux-gnu R Under development (unstable) (2020-01-08 r77640)
+* local R-devel-noLD:  x86_64-redhat-linux-gnu R Under development (unstable) (2020-01-08 r77640)
+* win-builder devel:   x86_64-w64-mingw32      R Under development (unstable) (2020-01-03 r77630)
+* win-builder release: x86_64-w64-mingw32      R 3.6.2 (2019-12-12)
+* rhub:       (debian) x86_64-pc-linux-gnu     R Under development (unstable) (2020-01-03 r77629)
 
 ## R CMD check results
 There were no ERRORs, WARNINGs, or NOTEs.