Date: Sat, 8 Jul 2023 03:50:04 GMT From: Joseph Mingrone <jrm@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 5fc301443c77 - main - biology/paml: Update to 4.10.7 Message-ID: <202307080350.3683o4wc094751@gitrepo.freebsd.org>
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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
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