git: 5fd436fa038a - main - biology/paml: Update to 4.10.9

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From: Joseph Mingrone <jrm_at_FreeBSD.org>
Date: Wed, 14 May 2025 16:53:45 UTC
The branch main has been updated by jrm:

URL: https://cgit.FreeBSD.org/ports/commit/?id=5fd436fa038a51191243a93ecb8a73c7514feace

commit 5fd436fa038a51191243a93ecb8a73c7514feace
Author:     Joseph Mingrone <jrm@FreeBSD.org>
AuthorDate: 2025-05-14 15:52:35 +0000
Commit:     Joseph Mingrone <jrm@FreeBSD.org>
CommitDate: 2025-05-14 15:59:29 +0000

    biology/paml: Update to 4.10.9
    
    Also patch out upstream's newly introduced hardcoded values for CC and
    CFLAGS.
    
    Release notes:  https://github.com/abacus-gene/paml/releases/tag/v4.10.8
                    https://github.com/abacus-gene/paml/releases/tag/v4.10.9
    Sponsored by:   The FreeBSD Foundation
---
 biology/paml/Makefile                 |  3 ++-
 biology/paml/distinfo                 |  6 +++---
 biology/paml/files/patch-src_Makefile | 15 ++++++++-------
 biology/paml/pkg-plist                |  2 --
 4 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/biology/paml/Makefile b/biology/paml/Makefile
index 7ba18e506f72..4a6375689d5e 100644
--- a/biology/paml/Makefile
+++ b/biology/paml/Makefile
@@ -1,5 +1,6 @@
 PORTNAME=	paml
-DISTVERSION=	4.10.7
+DISTVERSIONPREFIX=	v
+DISTVERSION=	4.10.9
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org
diff --git a/biology/paml/distinfo b/biology/paml/distinfo
index cd64f0e34127..7dd47591a370 100644
--- a/biology/paml/distinfo
+++ b/biology/paml/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1688759942
-SHA256 (abacus-gene-paml-4.10.7_GH0.tar.gz) = 0f29e768b3797b69eadc6332c3d046d8727702052d56c3b729883626c0a5a4e3
-SIZE (abacus-gene-paml-4.10.7_GH0.tar.gz) = 5250841
+TIMESTAMP = 1747232666
+SHA256 (abacus-gene-paml-v4.10.9_GH0.tar.gz) = 19ca9d484d729324748b9c86453e4c8f4a1fa79ad6fa3ac7cdbfaa7d0bfb8c22
+SIZE (abacus-gene-paml-v4.10.9_GH0.tar.gz) = 3920159
diff --git a/biology/paml/files/patch-src_Makefile b/biology/paml/files/patch-src_Makefile
index 4a9bd7ed2da6..1fd048a0594b 100644
--- a/biology/paml/files/patch-src_Makefile
+++ b/biology/paml/files/patch-src_Makefile
@@ -1,10 +1,11 @@
---- src/Makefile.orig	2023-07-08 03:40:50 UTC
+--- src/Makefile.orig	2025-05-14 14:29:51 UTC
 +++ src/Makefile
-@@ -1,6 +1,6 @@ CC = cc # cc, gcc, cl
+@@ -1,6 +1,6 @@ PRGS =  baseml codeml basemlg mcmctree pamp evolver yn
  PRGS =  baseml codeml basemlg mcmctree pamp evolver yn00 chi2
- CC = cc # cc, gcc, cl
--CFLAGS = -O3 -Wall -Wno-unused-result -Wmemset-elt-size
-+CFLAGS = -O3 -Wall -Wno-unused-result
- #CC = icc
- #CFLAGS = -fast -Wall
+-CC = gcc
+-CFLAGS = -O3 -Wall -Wno-unused-variable -Wno-unused-result
++#CC = gcc
++#CFLAGS = -O3 -Wall -Wno-unused-variable -Wno-unused-result
+ 
+ LIBS = -lm
  
diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist
index 544b761367c3..02f053d2563e 100644
--- a/biology/paml/pkg-plist
+++ b/biology/paml/pkg-plist
@@ -199,8 +199,6 @@ bin/yn00
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/data-MCU0.95-rep1.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/mlb-nhomo4.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/mlb-nhomo5.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/rst-nhomo4.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/rst-nhomo5.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/tree-nhomo4.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/tree-nhomo5.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl