Fix tests in case with no fftw support

inst/tests/test-mcmc.R

@@ -57,7 +57,7 @@ test_that("Likelihood function is saved with fit", {
   samples <- mcmc(lik, c(0, 0), 10, 1, print.every=0)
   expect_that(samples, has_attribute("func"))
   expect_that(attr(samples, "func"), is_a("function"))
-  expect_that(attr(samples, "func"), is_identical_to(lik))
+  expect_that(attr(samples, "func"), equals(lik))
 
   samples.no.func <- mcmc(lik, c(0, 0), 10, 1, print.every=0,
                           keep.func=FALSE)

inst/tests/test-ode.R

@@ -28,8 +28,8 @@ control.gslode.R <- check.control.ode(list(backend="gslode",
 control.deSolve <- check.control.ode(list(backend="deSolve"))
 
 ## Run the calculations with deSolve's lsoda (no clever tricks)
-res.ref <- lsoda(y, tt, derivs.for.deSolve(derivs), pars,
-                 atol=control.deSolve$tol, rtol=control.deSolve$tol)
+res.ref <- deSolve::lsoda(y, tt, derivs.for.deSolve(derivs), pars,
+                          atol=control.deSolve$tol, rtol=control.deSolve$tol)
 ## Convert this to the format that we expect (drop time column and
 ## transpose data).
 res.ref <- unname(t(res.ref[-1,-1,drop=FALSE]))
@@ -80,8 +80,8 @@ tm$set(pars.t)
 ## changes to tm.
 derivs.t <- make.derivs.t(derivs, tm)
 
-res.t.ref <- lsoda(y, tt, derivs.for.deSolve(derivs.t), pars,
-                   atol=control.deSolve$tol, rtol=control.deSolve$tol)
+res.t.ref <- deSolve::lsoda(y, tt, derivs.for.deSolve(derivs.t), pars,
+                            atol=control.deSolve$tol, rtol=control.deSolve$tol)
 res.t.ref <- unname(t(res.t.ref[-1,-1,drop=FALSE]))
 
 ## Quick check that this agrees with the original reference set, as
@@ -141,8 +141,8 @@ pars.t[c(2,4)] <- .01
 tm$set(pars.t)
 
 ## Rerun the above code
-res.t.ref <- lsoda(y, tt, derivs.for.deSolve(derivs.t), pars,
-                   atol=control.deSolve$tol, rtol=control.deSolve$tol)
+res.t.ref <- deSolve::lsoda(y, tt, derivs.for.deSolve(derivs.t), pars,
+                            atol=control.deSolve$tol, rtol=control.deSolve$tol)
 res.t.ref <- unname(t(res.t.ref[-1,-1,drop=FALSE]))
 
 ## Check that the reference example differs:

inst/tests/test-quasse-internal.R

@@ -65,6 +65,10 @@ for ( drift in c(0, .01) ) {
   expect_that(pars.fft$lo[1:5],          equals(pars.mol$lo[1:5]))
   expect_that(pars.fft$lo[1:5], is_identical_to(pars.mol$lo[1:5]))
 
+  ## Bail here if no FFTW support, even though we could do most of this.
+  if (!check.fftC(FALSE)) {
+    next
+  }
   pde.fftC <- with(control.fft, make.pde.quasse.fftC(nx, dx, dt.max, 2L, flags))
   pde.fftR <- with(control.fft, make.pde.quasse.fftR(nx, dx, dt.max, 2L))
   pde.mol <- with(control.mol, make.pde.quasse.mol(ndat, dx, 2L, atol, rtol))

inst/tests/test-quasse-split.R

@@ -21,6 +21,7 @@ control.C.2 <- c(control.C.1, tips.combined=TRUE)
 control.M.1 <- list(method="mol")
 control.R.1 <- list(dt.max=1/200, method="fftR")
 
+if (check.fftC(FALSE)) {
 lik.s <- make.quasse.split(phy, phy$tip.state, sd, sigmoid.x,
                            constant.x, "nd5", Inf, control.C.1)
 lik.q <- make.quasse(phy, phy$tip.state, sd, sigmoid.x, constant.x,
@@ -41,3 +42,4 @@ expect_that(lik.s(pars2.s), equals(ll.q))
 
 pars3.s <- pars + runif(length(pars.s), 0, .05)
 expect_that(lik.s(pars3.s), equals(-54.47383577050427))
+}

inst/tests/test-quasse.R

@@ -20,6 +20,7 @@ control.C.2 <- c(control.C.1, tips.combined=TRUE)
 control.M.1 <- list(method="mol")
 control.R.1 <- list(dt.max=1/200, method="fftR")
 
+if (check.fftC(FALSE)) {
 lik.C.1 <- make.quasse(phy, phy$tip.state, sd, sigmoid.x, constant.x,
                        control.C.1)
 ##lik.C.2 <- make.quasse(phy, phy$tip.state, sd, sigmoid.x, constant.x,
@@ -45,3 +46,4 @@ expect_that(lik.C.1(pars, root=ROOT.GIVEN, root.f=root.f),
 pars2 <- pars
 pars2[6] <- 0.01
 expect_that(lik.C.1(pars2), equals(-62.040165682569537))
+}