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 @@ -1,37 +1,39 @@ PORTNAME= lme4 -DISTVERSION= 2.0-1 +DISTVERSION= 2.0-6 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} MAINTAINER= eduardo@FreeBSD.org COMMENT= Linear mixed-effects models using Eigen and S4 WWW= https://cran.r-project.org/package=lme4 LICENSE= GPLv2+ 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= ${CRAN_DEPENDS} -TEST_DEPENDS= R-cran-ggplot2>0:graphics/R-cran-ggplot2 \ +TEST_DEPENDS= R-cran-car>0:math/R-cran-car \ + R-cran-ggplot2>0:graphics/R-cran-ggplot2 \ + R-cran-gridExtra>0:graphics/R-cran-gridExtra \ R-cran-knitr>0:print/R-cran-knitr \ R-cran-optimx>0:misc/R-cran-optimx \ R-cran-statmod>0:math/R-cran-statmod \ R-cran-testthat>0:devel/R-cran-testthat USES= cran:auto-plist,compiles pre-test: # Test depends not ported yet -.for pkg in gamm4 glmmTMB +.for pkg in DHARMa gamm4 glmmTMB mlmRev performance see @${LOCALBASE}/bin/Rscript -e 'install.packages("${pkg}", \ repos = "https://cloud.r-project.org")' .endfor .include 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 -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)