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biology/paml: Update to 4.10.7

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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
This commit is contained in:
Joseph Mingrone 2023-07-08 00:44:17 -03:00
parent 371eba15ec
commit 5fc301443c
No known key found for this signature in database
GPG Key ID: 36A40C83B0D6EF9E
4 changed files with 50 additions and 7 deletions
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3
biology/paml/Makefile
View File

@ -1,6 +1,5 @@
PORTNAME= paml
DISTVERSIONPREFIX= v
DISTVERSION= 4.10.6
DISTVERSION= 4.10.7
CATEGORIES= biology
MAINTAINER= jrm@FreeBSD.org

6
biology/paml/distinfo
View File

@ -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

10
biology/paml/files/patch-src_Makefile Normal file
View File

@ -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

38
biology/paml/pkg-plist
View File

@ -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