[Git][hardenedbsd/ports][hardenedbsd/main] 3 commits: math/R-cran-lme4: Fix tests

[HardenedBSD Services (@hardenedbsd-services)]

HardenedBSD Services pushed to branch hardenedbsd/main at HardenedBSD / Ports


Commits:
b4d7ad85 by Nuno Teixeira at 2026-03-08T01:19:19+00:00
math/R-cran-lme4: Fix tests

Apply upstream patch to fix tests.

- - - - -
04c14fd4 by Xin LI at 2026-03-07T20:28:31-08:00
archivers/lrzip: upgrade to 0.660.

- - - - -
0d0a2a8f by HardenedBSD Sync Services at 2026-03-08T00:00:46-07:00
Merge branch 'freebsd/main' into hardenedbsd/main

- - - - -


4 changed files:

- archivers/lrzip/Makefile
- archivers/lrzip/distinfo
- math/R-cran-lme4/Makefile
- + math/R-cran-lme4/files/patch-fix-test


Changes:

=====================================
archivers/lrzip/Makefile
=====================================
@@ -1,14 +1,18 @@
PORTNAME= lrzip
-PORTVERSION= 0.651
-PORTREVISION= 1
+DISTVERSIONPREFIX= v
+DISTVERSION= 0.660
CATEGORIES= archivers
-MASTER_SITES= http://ck.kolivas.org/apps/lrzip/

MAINTAINER= del...@FreeBSD.org
COMMENT= Long Range ZIP or Lzma RZIP

LICENSE= GPLv2

+USES= autoreconf cpe libtool perl5 shebangfix
+USE_GITHUB= yes
+GH_ACCOUNT= ckolivas
+GH_PROJECT= lrzip
+
BUILD_DEPENDS= nasm>=0:devel/nasm
LIB_DEPENDS= liblz4.so:archivers/liblz4 \
liblzo2.so:archivers/lzo2
@@ -18,10 +22,8 @@ CONFIGURE_ENV+= ac_cv_prog_ASM_PROG='no '
GNU_CONFIGURE= yes
GNU_CONFIGURE_MANPREFIX=${PREFIX}/share
LDFLAGS+= -L${LOCALBASE}/lib
-USES= cpe libtool perl5 shebangfix tar:xz
SHEBANG_FILES= ${WRKSRC}/lrztar
USE_PERL5= build
-USE_LDCONFIG= yes
CPE_VENDOR= lrzip_project

CONFLICTS_INSTALL= lrzsz # bin/lrz share/man/man1/lrz.1.gz


=====================================
archivers/lrzip/distinfo
=====================================
@@ -1,3 +1,3 @@
-TIMESTAMP = 1677886992
-SHA256 (lrzip-0.651.tar.xz) = 48bd8decb097c1596c9b3777959cd3e332819434ed77a2823e65aa436f1602f9
-SIZE (lrzip-0.651.tar.xz) = 416448
+TIMESTAMP = 1772270474
+SHA256 (ckolivas-lrzip-v0.660_GH0.tar.gz) = fd2cb18fc166e565a23f3415306d71a0f9151e0f1d7016d9a2c7eb038cd3c159
+SIZE (ckolivas-lrzip-v0.660_GH0.tar.gz) = 227127


=====================================
math/R-cran-lme4/Makefile
=====================================
@@ -26,8 +26,6 @@ TEST_DEPENDS= R-cran-ggplot2>0:graphics/R-cran-ggplot2 \

USES= cran:auto-plist,compiles

-TESTING_UNSAFE= https://github.com/lme4/lme4/issues/942
-
pre-test:

# Test depends not ported yet


=====================================
math/R-cran-lme4/files/patch-fix-test
=====================================
@@ -0,0 +1,31 @@
+From f1888c31db92f03c93d1bf05ecca1ac8a43c0935 Mon Sep 17 00:00:00 2001
+From: Ben Bolker <bbo...@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)



View it on GitLab: https://git.hardenedbsd.org/hardenedbsd/ports/-/compare/cd1463638bc6b85868166b8dd15b7323d863f2a0...0d0a2a8f5d3525b0ac11e1e4c338fcb1d6ed7eb9

--
View it on GitLab: https://git.hardenedbsd.org/hardenedbsd/ports/-/compare/cd1463638bc6b85868166b8dd15b7323d863f2a0...0d0a2a8f5d3525b0ac11e1e4c338fcb1d6ed7eb9
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