git: c5af67ba515c - main - math/R-cran-lme4: Update to 2.0-6

The branch main has been updated by eduardo:

URL: https://cgit.FreeBSD.org/ports/commit/?id=c5af67ba515cd4c59344354d7534c7f231673153

commit c5af67ba515cd4c59344354d7534c7f231673153
Author:     Nuno Teixeira <eduardo@FreeBSD.org>
AuthorDate: 2026-07-18 18:51:30 +0000
Commit:     Nuno Teixeira <eduardo@FreeBSD.org>
CommitDate: 2026-07-18 19:28:41 +0000

    math/R-cran-lme4: Update to 2.0-6
    
    ChangeLog: https://cran.r-project.org/web/packages/lme4/news.html
---
 math/R-cran-lme4/Makefile             | 10 ++++++----
 math/R-cran-lme4/distinfo             |  6 +++---
 math/R-cran-lme4/files/patch-fix-test | 31 -------------------------------
 3 files changed, 9 insertions(+), 38 deletions(-)

diff --git a/math/R-cran-lme4/Makefile b/math/R-cran-lme4/Makefile
index 5c06cbc5d011..b5cbfb9f8a41 100644
--- a/math/R-cran-lme4/Makefile
+++ b/math/R-cran-lme4/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	lme4
-DISTVERSION=	2.0-1
+DISTVERSION=	2.0-6
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
@@ -12,13 +12,15 @@ LICENSE_FILE=	${WRKSRC}/LICENSE.note
 
 CRAN_DEPENDS=	R-cran-minqa>=1.1.15:math/R-cran-minqa \
 		R-cran-nloptr>=1.0.4:math/R-cran-nloptr \
-		R-cran-Rcpp>=0.10.5:devel/R-cran-Rcpp \
+		R-cran-Rcpp>=1.1.1.1.1:devel/R-cran-Rcpp \
 		R-cran-RcppEigen>=0.3.3.9.4:math/R-cran-RcppEigen \
 		R-cran-reformulas>=0.4.3.1:math/R-cran-reformulas \
 		R-cran-rlang>0:devel/R-cran-rlang
 BUILD_DEPENDS=	${CRAN_DEPENDS}
 RUN_DEPENDS=	${CRAN_DEPENDS}
-TEST_DEPENDS=	R-cran-ggplot2>0:graphics/R-cran-ggplot2 \
+TEST_DEPENDS=	R-cran-car>0:math/R-cran-car \
+		R-cran-ggplot2>0:graphics/R-cran-ggplot2 \
+		R-cran-gridExtra>0:graphics/R-cran-gridExtra \
 		R-cran-knitr>0:print/R-cran-knitr \
 		R-cran-optimx>0:misc/R-cran-optimx \
 		R-cran-statmod>0:math/R-cran-statmod \
@@ -29,7 +31,7 @@ USES=		cran:auto-plist,compiles
 pre-test:
 
 # Test depends not ported yet
-.for pkg in gamm4 glmmTMB
+.for pkg in DHARMa gamm4 glmmTMB mlmRev performance see
 	@${LOCALBASE}/bin/Rscript -e 'install.packages("${pkg}", \
 		repos = "https://cloud.r-project.org")'
 .endfor
diff --git a/math/R-cran-lme4/distinfo b/math/R-cran-lme4/distinfo
index 91daaf122a2e..5aaec5f87b30 100644
--- a/math/R-cran-lme4/distinfo
+++ b/math/R-cran-lme4/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1772823526
-SHA256 (lme4_2.0-1.tar.gz) = a34b75c1ef05d7c023d9d86c9d644381a4098de5b3008f9256b89b3a380917a4
-SIZE (lme4_2.0-1.tar.gz) = 3701223
+TIMESTAMP = 1784370005
+SHA256 (lme4_2.0-6.tar.gz) = 3e503bc10626ad62804c80a82237147b1296d93c18d88946554c29075af917f7
+SIZE (lme4_2.0-6.tar.gz) = 4266192
diff --git a/math/R-cran-lme4/files/patch-fix-test b/math/R-cran-lme4/files/patch-fix-test
deleted file mode 100644
index 1d1baacb55b1..000000000000
--- a/math/R-cran-lme4/files/patch-fix-test
+++ /dev/null
@@ -1,31 +0,0 @@
-From f1888c31db92f03c93d1bf05ecca1ac8a43c0935 Mon Sep 17 00:00:00 2001
-From: Ben Bolker <bbolker@gmail.com>
-Date: Sat, 7 Mar 2026 10:59:42 -0500
-Subject: [PATCH] loosen tolerance in isSingular test [run ci]
-
----
- tests/testthat/test-isSingular.R | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git tests/testthat/test-isSingular.R tests/testthat/test-isSingular.R
-index 33d47579..7d41562a 100644
---- tests/testthat/test-isSingular.R
-+++ tests/testthat/test-isSingular.R
-@@ -21,7 +21,7 @@ test_that("checking singular fit for covariance", {
-   
-   test.reCovs <- c(test.us, test.diag, test.cs, test.homcs, test.ar1, test.hetar1)
-   
--  ## tests should fail once one of the diagional entries is 0
-+  ## tests should fail once one of the diagonal entries is 0
-   sapply(test.reCovs, function(i){
-     new_theta <- getTheta(i)
-     new_theta[1] <- 0
-@@ -74,7 +74,7 @@ test_that("checking singular fit for merMod", {
-                                      sigma = 2))[[1]]
-   mod2 <- suppressWarnings(lmer(form2, data = dat))
-   ## second one, should be an issue with group 1 as we set thetas = 0
--  expect_equal(isSingular(mod2), TRUE)
-+  expect_equal(isSingular(mod2, tol = 5e-4), TRUE)
-   
-   ## also need to consider the glmer case
-   form <- y ~ 1 + (1 + x1 | group1) + (1 + x2 | group2)