R Under development (unstable) (2024-06-05 r86695 ucrt) -- "Unsuffered Consequences"
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> ## PR#16744: ordering of variance weights (failed in nlme <= 3.1-149)
> library("nlme")
> fm3 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
+            correlation = corAR1(form = ~ 1 | Mare),
+            weights = ~as.integer(as.character(Mare)))  # fixed variance weights
> stopifnot(
+     identical(
+         getVarCov(fm3, individual = 3),
+         getVarCov(fm3, individual = levels(Ovary$Mare)[3])
+     ),
+     all.equal(
+         vapply(as.character(1:11),
+                function (id) getVarCov(fm3, individual = id)[1,1],
+                0, USE.NAMES = FALSE),
+         fm3$sigma^2 * (1:11)
+     )
+ )
> 
> ## lme method had a similar issue for data not ordered by levels(group)
> ## is.unsorted(Orthodont$Subject)  # TRUE
> fm4 <- lme(distance ~ age, Orthodont, weights = ~as.integer(Subject))
> covmats <- getVarCov(fm4, individuals = levels(Orthodont$Subject),
+                      type = "conditional")
> stopifnot(
+     all.equal(
+         vapply(covmats, "[", 0, 1, 1),
+         fm4$sigma^2 * seq_len(nlevels(Orthodont$Subject)),
+         check.attributes = FALSE
+     )
+ )
> 
> 
> ## PR#16806: 1-observation groups in corSpatial fits (failed in nlme <= 3.1-164)
> data("Phenobarb")
> pheno <- subset(Phenobarb, !is.na(conc))
> stopifnot(sum(getGroups(pheno) == "28") == 1) # Subject 28 has only 1 obs.
> lme1 <- lme(conc ~ time, data = pheno, random = ~1 | Subject,
+             correlation = corExp(form = ~time | Subject))
> condVarCov <- getVarCov(lme1, type = "conditional", individuals = "28")
> ## gave Error in dimnames(cond.var) <- list(1:nrow(cond.var), 1:ncol(cond.var)) :
> ##   length of 'dimnames' [2] not equal to array extent
> stopifnot(all.equal(unname(diag(condVarCov[[1]])), lme1$sigma^2))
> ## same for gls():
> gls1 <- gls(conc ~ time, data = pheno,
+             correlation = corExp(form = ~time | Subject))
> margVarCov <- getVarCov(gls1, individual = "28")
> ## gave Error in rep(1, nrow(S)) : invalid 'times' argument
> stopifnot(all.equal(diag(margVarCov), gls1$sigma^2))
> 
> proc.time()
   user  system elapsed 
   0.43    0.07    0.45