Running examples in ‘asremlPlus-Ex.R’ failed
The error most likely occurred in:

> ### Name: linTransform.alldiffs
> ### Title: Calculates a linear transformation of the predictions stored in
> ###   an 'alldiffs.object'.
> ### Aliases: linTransform.alldiffs linTransform
> ### Keywords: asreml
> 
> ### ** Examples
> 
> data(WaterRunoff.dat)
> 
> ##Use asreml to get predictions and associated statistics
> 
> ## Not run: 
> ##D asreml.options(keep.order = TRUE) #required for asreml-R4 only
> ##D current.asr <- asreml(fixed = pH ~ Benches + (Sources * (Type + Species)), 
> ##D                       random = ~ Benches:MainPlots,
> ##D                       keep.order=TRUE, data= WaterRunoff.dat)
> ##D current.asrt <- as.asrtests(current.asr, NULL, NULL)
> ##D #Get additive predictions directly using predictPlus
> ##D diffs.sub <- predictPlus.asreml(classify = "Sources:Species", Vmatrix = TRUE, 
> ##D                                 linear.transformation = ~ Sources + Species,
> ##D                                 asreml.obj = current.asr, tables = "none", 
> ##D                                 wald.tab = current.asrt$wald.tab, 
> ##D                                 present = c("Type","Species","Sources"))
> ## End(Not run)
> 
> ## Use lmeTest and emmmeans to get predictions and associated statistics
> 
> if (requireNamespace("lmerTest", quietly = TRUE) & 
+     requireNamespace("emmeans", quietly = TRUE))
+ {
+   m1.lmer <- lmerTest::lmer(pH ~ Benches + (Sources * Species) + 
+                               (1|Benches:MainPlots),
+                             data=na.omit(WaterRunoff.dat))
+   SS.emm <- emmeans::emmeans(m1.lmer, specs = ~ Sources:Species)
+   SS.preds <- summary(SS.emm)
+   den.df <- min(SS.preds$df, na.rm = TRUE)
+   ## Modify SS.preds to be compatible with a predictions.frame
+   SS.preds <- as.predictions.frame(SS.preds, predictions = "emmean", 
+                                    se = "SE", interval.type = "CI", 
+                                    interval.names = c("lower.CL", "upper.CL"))
+   
+   ## Form an all.diffs object and check its validity
+   SS.vcov <- vcov(SS.emm)
+   SS.diffs <- allDifferences(predictions = SS.preds, classify = "Sources:Species", 
+                              vcov = SS.vcov, tdf = den.df)
+   validAlldiffs(SS.diffs)
+ 
+   #Get additive predictions
+   diffs.sub <- linTransform(SS.diffs, classify = "Sources:Species", 
+                             linear.transformation = ~ Sources + Species,
+                             Vmatrix = TRUE, tables = "none")
+ }  
fixed-effect model matrix is rank deficient so dropping 8 columns / coefficients
Warning in qr2rankMatrix(q.r, tol = tol, isBqr = x.dense, do.warn = warn.qr) :
  qr2rankMatrix(.): QR has negative diag(R) entries
Error: Dropping columns failed to produce full column rank design matrix
Execution halted