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biology/paml: Update to 4.10.9

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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
This commit is contained in:
Joseph Mingrone 2025-05-14 12:52:35 -03:00
parent 354804d247
commit 5fd436fa03
No known key found for this signature in database
GPG Key ID: 36A40C83B0D6EF9E
4 changed files with 13 additions and 13 deletions
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3
biology/paml/Makefile
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@ -1,5 +1,6 @@
PORTNAME= paml PORTNAME= paml
DISTVERSION= 4.10.7 DISTVERSIONPREFIX= v
DISTVERSION= 4.10.9
CATEGORIES= biology CATEGORIES= biology
MAINTAINER= jrm@FreeBSD.org MAINTAINER= jrm@FreeBSD.org

6
biology/paml/distinfo
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@ -1,3 +1,3 @@
TIMESTAMP = 1688759942 TIMESTAMP = 1747232666
SHA256 (abacus-gene-paml-4.10.7_GH0.tar.gz) = 0f29e768b3797b69eadc6332c3d046d8727702052d56c3b729883626c0a5a4e3 SHA256 (abacus-gene-paml-v4.10.9_GH0.tar.gz) = 19ca9d484d729324748b9c86453e4c8f4a1fa79ad6fa3ac7cdbfaa7d0bfb8c22
SIZE (abacus-gene-paml-4.10.7_GH0.tar.gz) = 5250841 SIZE (abacus-gene-paml-v4.10.9_GH0.tar.gz) = 3920159

15
biology/paml/files/patch-src_Makefile
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@ -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 +++ 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 PRGS = baseml codeml basemlg mcmctree pamp evolver yn00 chi2
CC = cc # cc, gcc, cl -CC = gcc
-CFLAGS = -O3 -Wall -Wno-unused-result -Wmemset-elt-size -CFLAGS = -O3 -Wall -Wno-unused-variable -Wno-unused-result
+CFLAGS = -O3 -Wall -Wno-unused-result +#CC = gcc
#CC = icc +#CFLAGS = -O3 -Wall -Wno-unused-variable -Wno-unused-result
#CFLAGS = -fast -Wall
LIBS = -lm

2
biology/paml/pkg-plist
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@ -199,8 +199,6 @@ bin/yn00
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/data-MCU0.95-rep1.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/data-MCU0.95-rep1.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/mlb-nhomo4.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/mlb-nhomo4.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/mlb-nhomo5.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-nhomo4.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/tree-nhomo5.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/tree-nhomo5.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl