git: 5fc301443c77 - main - biology/paml: Update to 4.10.7

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From: Joseph Mingrone <jrm_at_FreeBSD.org>
Date: Sat, 08 Jul 2023 03:50:04 UTC
The branch main has been updated by jrm:

URL: https://cgit.FreeBSD.org/ports/commit/?id=5fc301443c77a4952c42153f12a7520f913f60a3

commit 5fc301443c77a4952c42153f12a7520f913f60a3
Author:     Joseph Mingrone <jrm@FreeBSD.org>
AuthorDate: 2023-07-08 03:44:17 +0000
Commit:     Joseph Mingrone <jrm@FreeBSD.org>
CommitDate: 2023-07-08 03:46:53 +0000

    biology/paml: Update to 4.10.7
    
    Remove -Wmemset-elt-size from CFLAGS.  The warning is only applicable to
    gcc and is already enabled with -Wall.
    
    Changes:        https://github.com/abacus-gene/paml/releases/tag/4.10.7
    Sponsored by:   The FreeBSD Foundation
---
 biology/paml/Makefile                 |  3 +--
 biology/paml/distinfo                 |  6 +++---
 biology/paml/files/patch-src_Makefile | 10 +++++++++
 biology/paml/pkg-plist                | 38 +++++++++++++++++++++++++++++++++--
 4 files changed, 50 insertions(+), 7 deletions(-)

diff --git a/biology/paml/Makefile b/biology/paml/Makefile
index 6a0b8081fd19..7ba18e506f72 100644
--- a/biology/paml/Makefile
+++ b/biology/paml/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	paml
-DISTVERSIONPREFIX=	v
-DISTVERSION=	4.10.6
+DISTVERSION=	4.10.7
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org
diff --git a/biology/paml/distinfo b/biology/paml/distinfo
index f597c10ced71..cd64f0e34127 100644
--- a/biology/paml/distinfo
+++ b/biology/paml/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1668305503
-SHA256 (abacus-gene-paml-v4.10.6_GH0.tar.gz) = d6437f04ee233209e1ded83addbfe65d1363185877a03ba7924ce81f9ebc7777
-SIZE (abacus-gene-paml-v4.10.6_GH0.tar.gz) = 3386016
+TIMESTAMP = 1688759942
+SHA256 (abacus-gene-paml-4.10.7_GH0.tar.gz) = 0f29e768b3797b69eadc6332c3d046d8727702052d56c3b729883626c0a5a4e3
+SIZE (abacus-gene-paml-4.10.7_GH0.tar.gz) = 5250841
diff --git a/biology/paml/files/patch-src_Makefile b/biology/paml/files/patch-src_Makefile
new file mode 100644
index 000000000000..4a9bd7ed2da6
--- /dev/null
+++ b/biology/paml/files/patch-src_Makefile
@@ -0,0 +1,10 @@
+--- src/Makefile.orig	2023-07-08 03:40:50 UTC
++++ src/Makefile
+@@ -1,6 +1,6 @@ CC = cc # cc, gcc, cl
+ 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
+ 
diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist
index aac062f86730..544b761367c3 100644
--- a/biology/paml/pkg-plist
+++ b/biology/paml/pkg-plist
@@ -44,9 +44,13 @@ bin/yn00
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/codeml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCaa.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCaa.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbase.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbase.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbaseRandomTree.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbaseRandomTree.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCcodon.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCcodon.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.phy
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.trees
@@ -126,6 +130,12 @@ bin/yn00
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtREV24.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtmam.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/wag.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/6s-bracing.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/6s.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/MCbase-6s.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/mc.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/mcmctree-bracing.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/mcmctree.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/README.txt
@@ -165,10 +175,34 @@ bin/yn00
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtprim9.nuc
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-mc.trees
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-mc.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/codeml-M0.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/myxovirus.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/myxovirus.tree
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata-maintree.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/5s-mc.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/MCbase.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata-maintree-ml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata-maintree.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata-maintree-ml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata-maintree.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/mc.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/baseml-nhomo4.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/baseml-nhomo5.ctl
+%%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
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupblock
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupend