Bug 294891

Summary: biology/muscle: update 3.8.1551 -> 5.1
Product: Ports & Packages Reporter: Rodrigo Osorio <rodrigo>
Component: Individual Port(s)Assignee: Rodrigo Osorio <rodrigo>
Status: Closed FIXED    
Severity: Affects Only Me CC: mzaki
Priority: --- Flags: bugzilla: maintainer-feedback? (mzaki)
Version: Latest   
Hardware: Any   
OS: Any   
Attachments:
Description Flags
muscle 5.1 update none

Description Rodrigo Osorio freebsd_committer freebsd_triage 2026-04-30 08:25:44 UTC 
Created attachment 270262 [details]
muscle 5.1 update

In 2021, the code was re-written from scratch for MUSCLE v5 to implement novel algorithms and fully support modern PC hardware.

https://drive5.com/muscle5/
Comment 1 commit-hook freebsd_committer freebsd_triage 2026-07-21 09:53:08 UTC 
A commit in branch main references this bug:

URL: https://cgit.FreeBSD.org/ports/commit/?id=6c7bfd6a6aab06279041e5d5b9c63a1dec8a24dd

commit 6c7bfd6a6aab06279041e5d5b9c63a1dec8a24dd
Author:     Rodrigo Osorio <rodrigo@FreeBSD.org>
AuthorDate: 2026-07-20 13:08:11 +0000
Commit:     Rodrigo Osorio <rodrigo@FreeBSD.org>
CommitDate: 2026-07-21 09:50:28 +0000

    biology/muscle: update 3.8.1551 -> 5.1

    In 2021, the code was re-written from scratch for MUSCLE v5 to implement
    novel algorithms and fully support modern PC hardware.

    PR:             294891
    Approved by: Maintainer Timeout (>2 months)

 biology/muscle/Makefile                            | 26 +++---
 biology/muscle/distinfo                            |  6 +-
 biology/muscle/files/patch-Makefile (gone)         | 28 -------
 biology/muscle/files/patch-globalslinux.cpp (gone) | 94 ----------------------
 biology/muscle/files/patch-src__myutils.cpp (new)  | 65 +++++++++++++++
 5 files changed, 83 insertions(+), 136 deletions(-)
Comment 2 Rodrigo Osorio freebsd_committer freebsd_triage 2026-07-21 10:01:15 UTC 
Committed under maintainer Timeout
Comment 3 commit-hook freebsd_committer freebsd_triage 2026-07-24 17:48:43 UTC 
A commit in branch main references this bug:

URL: https://cgit.FreeBSD.org/ports/commit/?id=7b7b1a9a84e4e34dd26715e9b28d9e57569492be

commit 7b7b1a9a84e4e34dd26715e9b28d9e57569492be
Author:     Rodrigo Osorio <rodrigo@FreeBSD.org>
AuthorDate: 2026-07-20 13:08:11 +0000
Commit:     Rodrigo Osorio <rodrigo@FreeBSD.org>
CommitDate: 2026-07-21 09:50:28 +0000

    biology/muscle: update 3.8.1551 -> 5.1

    In 2021, the code was re-written from scratch for MUSCLE v5 to implement
    novel algorithms and fully support modern PC hardware.

    PR:             294891
    Approved by: Maintainer Timeout (>2 months)

 biology/muscle/Makefile                            | 26 +++---
 biology/muscle/distinfo                            |  6 +-
 biology/muscle/files/patch-Makefile (gone)         | 28 -------
 biology/muscle/files/patch-globalslinux.cpp (gone) | 94 ----------------------
 biology/muscle/files/patch-src__myutils.cpp (new)  | 65 +++++++++++++++
 5 files changed, 83 insertions(+), 136 deletions(-)