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

> ### Name: recalcLSD.alldiffs
> ### Title: Adds or recalculates the 'LSD.frame' that is a component of an
> ###   'alldiffs.object'.
> ### Aliases: recalcLSD.alldiffs recalcLSD
> ### 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 TS.diffs <- predictPlus(classify = "Sources:Type", 
> ##D                         asreml.obj = current.asr, 
> ##D                         wald.tab = current.asrt$wald.tab, 
> ##D                         present = c("Sources", "Type", "Species"))
> ## End(Not run)
> 
> ## Use lmeTest and emmmeans to get predictions and associated statistics
> 
> if (requireNamespace("lmerTest", quietly = TRUE) & 
+     requireNamespace("emmeans", quietly = TRUE))
+ {
+   m1.lmer <- lmerTest::lmer(pH ~ Benches + (Sources * (Type + Species)) + 
+                               (1|Benches:MainPlots),
+                             data=na.omit(WaterRunoff.dat))
+   TS.emm <- emmeans::emmeans(m1.lmer, specs = ~ Sources:Species)
+   TS.preds <- summary(TS.emm)
+   den.df <- min(TS.preds$df, na.rm = TRUE)
+   ## Modify TS.preds to be compatible with a predictions.frame
+   TS.preds <- as.predictions.frame(TS.preds, predictions = "emmean", 
+                                    se = "SE", interval.type = "CI", 
+                                    interval.names = c("lower.CL", "upper.CL"))
+   
+   ## Form an all.diffs object and check its validity
+   els <- as.numeric(rownames(TS.preds))
+   TS.vcov <- vcov(TS.emm)[els,els]
+   TS.diffs <- allDifferences(predictions = TS.preds, classify = "Sources:Species", 
+                              vcov = TS.vcov, tdf = den.df)
+   validAlldiffs(TS.diffs)
+ }  
fixed-effect model matrix is rank deficient so dropping 26 columns / coefficients
boundary (singular) fit: see help('isSingular')
NOTE: A nesting structure was detected in the fitted model:
    Species %in% Type
Error in vcov(TS.emm)[els, els] : subscript out of bounds
Execution halted