Created attachment 257423 [details] [PATCH] biology/iqtree: update 2.3.6 => 2.4.0 Version 2.4.0 Latest This release includes a major bug fix of AliSim (Bug ID #333). This bug occurred due to the use of identical random seed numbers for generating the root sequence and simulating its first descendant sequence, which resulted in identical sequences at the root and its first child node. For more detailed information about the bug, its effects, the impacted release versions, and a list of papers that might be affected, please refer to our comprehensive bug report. We apologize for any inconvenience this bug may have caused.
Thanks. I already have a WIP branch that's going through testing. I'm just waiting for poudriere to finish. However, I do prefer your patch to disable that annoying build-time-download dependency on googletest, so I'll incorporate that.
A commit in branch main references this bug: URL: https://cgit.FreeBSD.org/ports/commit/?id=6ac077207c4d64cfa0b22fb8c041c2114f7f89c6 commit 6ac077207c4d64cfa0b22fb8c041c2114f7f89c6 Author: Joseph Mingrone <jrm@FreeBSD.org> AuthorDate: 2025-02-12 14:42:08 +0000 Commit: Joseph Mingrone <jrm@FreeBSD.org> CommitDate: 2025-02-12 15:08:27 +0000 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 <alster@vinterdalen.se> biology/iqtree/Makefile | 11 +++++------ biology/iqtree/distinfo | 12 +++++++----- .../iqtree/files/patch-cmaple_unittest_CMakeLists.txt (new) | 10 ++++++++++ 3 files changed, 22 insertions(+), 11 deletions(-)