clean up tests [run ci]

R/plot.R

@@ -434,8 +434,6 @@ qqmath.merMod <- function(x, data = NULL, id=NULL, idLabels=NULL, ...) {
     if (!is.null(data)) {
         idLabels <- id
         id <- data
-        print(id)
-        print(idLabels)
         warning("qqmath.merMod takes ", sQuote("data"), "as its ",
                 "first argument for S3 method compatibility: ",
                 "in the future, please ",

R/predict.R

@@ -503,8 +503,12 @@ predict.merMod <- function(object, newdata=NULL, newparams=NULL,
             newRE <- mkNewReTrms(object, rfd, re.form, na.action=na.action,
                                  allow.new.levels=allow.new.levels)
             REvals <- base::drop(as(newRE$b %*% newRE$Zt, "matrix"))
-            if (class(fit.na.action) %in% c("omit", "exclude") && length(fit.na.action)>0) {
-                REvals <- REvals[-fit.na.action]
+            ## only needed if called as simulation? NAs sometimes excluded within mkNewReTrms ...
+            if (length(pred) != length(REvals)) {
+                if (!class(fit.na.action) %in% c("omit", "exclude") && length(fit.na.action)>0) {
+                    stop("fixed/RE pred length mismatch")
+                }                    
+                 REvals <- REvals[-fit.na.action]
             }
             pred <- pred + REvals
             if (random.only) {

src/Makevars

@@ -1,6 +1,5 @@
 ## -*- mode: makefile; -*-
 
-PKG_LIBS = `$(R_HOME)/bin/Rscript --vanilla -e "Rcpp:::LdFlags()"`
 PKG_CXXFLAGS = -DEIGEN_DONT_VECTORIZE
 
 ## For a release, uncomment the following line to suppress package

tests/testthat/test-methods.R

@@ -685,8 +685,8 @@ test_that("plot", {
                 (1|recipe:replicate), cake2, REML= FALSE)
   expect_is(lattice::qqmath(fm2, id=0.05), "trellis")
   expect_is(lattice::qqmath(fm2, id=0.05, idLabels=~recipe), "trellis")
-  expect_is(lattice::qqmath(fm2, 0.05, ~recipe), "trellis") # was expect_warning()
-  expect_is(lattice::qqmath(fm2, 0.05),          "trellis") # was expect_warning()
+  expect_warning(lattice::qqmath(fm2, 0.05, ~recipe), "please specify")
+  expect_warning(lattice::qqmath(fm2, 0.05),          "please specify")
 })
 
 context("misc")

tests/testthat/test-predict.R

@@ -498,20 +498,23 @@ test_that("predict works with factors in left-out REs", {
                       lc = factor(rep(1:2, 50)),
                       g1 = factor(rep(1:10, 10)),
                       g3 = factor(rep(1:10, each = 10)))
-    m1B <- lmer(yield ~ 1 + ( 1 | g1) + (lc |g3), data  = df2)
+    m1B <- lmer(yield ~ 1 + ( 1 | g1) + (lc |g3), data  = df2,
+                control = lmerControl(check.conv.singular = "ignore"))
     expect_equal(head(predict(m1B, re.form = ~(1|g1)),1),
                  c(`1` = 0.146787496519465))
 })
 
 test_that("predict works with dummy() in left-out REs", {
+    set.seed(101)
     df3 <- data.frame(v1 = rnorm(100),
        		  v3 = factor(rep(1:10, each = 10)),
 		  v4 = factor(rep(1:2, each = 50)),
 		  v5 = factor(rep(1:10, 10)))
     m1C  <- lmer(v1~(1|v3) + (0+dummy(v4,"1")|v5),
                  data = df3,
                  control=lmerControl(check.nobs.vs.nlev="ignore",
-                                     check.nobs.vs.nRE="ignore"))
+                                     check.nobs.vs.nRE="ignore",
+                                     check.conv.singular = "ignore"))
     expect_equal(head(predict(m1C, re.form = ~1|v3), 1),
-                 c(`1` = 0.0354183724049692))
+                 c(`1` = -0.035719520719991))
 })