From 6ac077207c4d64cfa0b22fb8c041c2114f7f89c6 Mon Sep 17 00:00:00 2001 From: Joseph Mingrone Date: Wed, 12 Feb 2025 10:42:08 -0400 Subject: [PATCH] biology/iqtree: Update to 2.4.0 Refer to the release notes for information about a bug that may impact past results. PR: 284746 Release Notes: https://github.com/iqtree/iqtree2/releases/tag/v2.4.0 Sponsored by: The FreeBSD Foundation Co-authored-by: Alven --- biology/iqtree/Makefile | 11 +++++------ biology/iqtree/distinfo | 12 +++++++----- .../files/patch-cmaple_unittest_CMakeLists.txt | 10 ++++++++++ 3 files changed, 22 insertions(+), 11 deletions(-) create mode 100644 biology/iqtree/files/patch-cmaple_unittest_CMakeLists.txt diff --git a/biology/iqtree/Makefile b/biology/iqtree/Makefile index 484da90fa48f..edaf3f6f4603 100644 --- a/biology/iqtree/Makefile +++ b/biology/iqtree/Makefile @@ -1,7 +1,6 @@ PORTNAME= iqtree DISTVERSIONPREFIX= v -DISTVERSION = 2.3.6 -PORTREVISION= 2 +DISTVERSION= 2.4.0 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org @@ -12,17 +11,17 @@ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_aarch64= fails to compile: unrecognized command line option '-msse3' -BROKEN_armv6= fails to compile: unrecognized command line options '-m32' and '-msse3' -BROKEN_armv7= fails to compile: unrecognized command line options '-m32' and '-msse3' -BROKEN_i386= ld: error: unable to find library -latomic (see bug 230888) BROKEN_powerpc64= fails to build: GCC version must be at least 4.8! +NOT_FOR_ARCHS= armv6 armv7 i386 powerpc +NOT_FOR_ARCHS_REASON= 32-bit compilation is not supported LIB_DEPENDS= libboost_filesystem.so:devel/boost-libs USES= cmake eigen:3 USE_GITHUB= yes GH_PROJECT= iqtree2 -GH_TUPLE= tothuhien:lsd2:125720d9da1281642053713d9b094d5bff2ce9cf:tothuhien/lsd2 +GH_TUPLE= tothuhien:lsd2:c61110f3a4fa05325b45c97b2134792ff9d55d4c:tothuhien/lsd2 \ + iqtree:cmaple:3946f47731699573ed2268e00aa7996a3458d4eb:iqtree/cmaple PLIST_FILES= bin/iqtree PORTEXAMPLES= custom_distributions.txt example.cf example.nex example.phy \ diff --git a/biology/iqtree/distinfo b/biology/iqtree/distinfo index c04b15ab879a..ae72ac55ee39 100644 --- a/biology/iqtree/distinfo +++ b/biology/iqtree/distinfo @@ -1,5 +1,7 @@ -TIMESTAMP = 1725465363 -SHA256 (iqtree-iqtree2-v2.3.6_GH0.tar.gz) = 2d389ea74e19773496363cd68270b341ac7cc47c60e7f32859682403b34744cf -SIZE (iqtree-iqtree2-v2.3.6_GH0.tar.gz) = 6644218 -SHA256 (tothuhien-lsd2-125720d9da1281642053713d9b094d5bff2ce9cf_GH0.tar.gz) = acab6984ceeb1e1c45f87bfb30cadd18c29b48088912e80521e8c875ce33a50b -SIZE (tothuhien-lsd2-125720d9da1281642053713d9b094d5bff2ce9cf_GH0.tar.gz) = 592579 +TIMESTAMP = 1739123157 +SHA256 (iqtree-iqtree2-v2.4.0_GH0.tar.gz) = 06a3351de0ed3c44a3e197e94a5d0cc3de7359c0be79eab1f41fb83459234619 +SIZE (iqtree-iqtree2-v2.4.0_GH0.tar.gz) = 5524827 +SHA256 (tothuhien-lsd2-c61110f3a4fa05325b45c97b2134792ff9d55d4c_GH0.tar.gz) = 9bbeaa0f8f35783c1d8dec74df6c93a804dbca808fa04484f9123de4e7258b53 +SIZE (tothuhien-lsd2-c61110f3a4fa05325b45c97b2134792ff9d55d4c_GH0.tar.gz) = 1529381 +SHA256 (iqtree-cmaple-3946f47731699573ed2268e00aa7996a3458d4eb_GH0.tar.gz) = 712016835e40c26c1e69529fca1bec46a7102ede3775e1b4b6589c4b6074410a +SIZE (iqtree-cmaple-3946f47731699573ed2268e00aa7996a3458d4eb_GH0.tar.gz) = 4806755 diff --git a/biology/iqtree/files/patch-cmaple_unittest_CMakeLists.txt b/biology/iqtree/files/patch-cmaple_unittest_CMakeLists.txt new file mode 100644 index 000000000000..d28f9256b534 --- /dev/null +++ b/biology/iqtree/files/patch-cmaple_unittest_CMakeLists.txt @@ -0,0 +1,10 @@ +--- cmaple/unittest/CMakeLists.txt.orig 2025-02-11 20:40:54 UTC ++++ cmaple/unittest/CMakeLists.txt +@@ -16,7 +16,6 @@ target_link_libraries( + ) + target_link_libraries( + cmaple_maintest +- GTest::gtest_main ## contains the main() function. No need to write one yourself + cmaple_utils + ncl nclextra + cmaple_model