svn commit: r482495 - head/biology/hyphy
Joseph Mingrone
jrm at FreeBSD.org
Sat Oct 20 12:21:16 UTC 2018
Author: jrm
Date: Sat Oct 20 12:21:15 2018
New Revision: 482495
URL: https://svnweb.freebsd.org/changeset/ports/482495
Log:
biology/hyphy: Update to version 2.3.14.16
This pulls in fixes after the 2.3.14 release.
Upstream changes for version 2.3.14:
https://github.com/veg/hyphy/releases/tag/2.3.14
Subsequent fixes:
https://github.com/veg/hyphy/commit/1ecac31
https://github.com/veg/hyphy/commit/bec6833
https://github.com/veg/hyphy/commit/9847438
https://github.com/veg/hyphy/commit/02dcedd
https://github.com/veg/hyphy/commit/8f44d3c
https://github.com/veg/hyphy/commit/5297c30
https://github.com/veg/hyphy/commit/3d88d3e
Modified:
head/biology/hyphy/Makefile (contents, props changed)
head/biology/hyphy/distinfo (contents, props changed)
head/biology/hyphy/pkg-plist (contents, props changed)
Modified: head/biology/hyphy/Makefile
==============================================================================
--- head/biology/hyphy/Makefile Sat Oct 20 12:14:02 2018 (r482494)
+++ head/biology/hyphy/Makefile Sat Oct 20 12:21:15 2018 (r482495)
@@ -1,7 +1,8 @@
# $FreeBSD$
PORTNAME= hyphy
-DISTVERSION= 2.3.13
+DISTVERSION= 2.3.14-16
+DISTVERSIONSUFFIX= -g3d88d3e6
CATEGORIES= biology
MAINTAINER= jrm at FreeBSD.org
@@ -17,5 +18,7 @@ LIB_DEPENDS= libcurl.so:ftp/curl
USES= compiler:c++14-lang cmake:outsource localbase:ldflags ssl
USE_GITHUB= yes
GH_ACCOUNT= veg
+
+CMAKE_ON= NOAVX
.include <bsd.port.mk>
Modified: head/biology/hyphy/distinfo
==============================================================================
--- head/biology/hyphy/distinfo Sat Oct 20 12:14:02 2018 (r482494)
+++ head/biology/hyphy/distinfo Sat Oct 20 12:21:15 2018 (r482495)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1527024059
-SHA256 (veg-hyphy-2.3.13_GH0.tar.gz) = 29b72574302c98d38a92d5316b9283caa80a54c3e74c5e278c5bc9ae3d3df499
-SIZE (veg-hyphy-2.3.13_GH0.tar.gz) = 7910770
+TIMESTAMP = 1540036335
+SHA256 (veg-hyphy-2.3.14-16-g3d88d3e6_GH0.tar.gz) = 459cd0a261ae5f31dc230847acbd294a4dc1e17fa69ef0c3db173c2b8808c826
+SIZE (veg-hyphy-2.3.14-16-g3d88d3e6_GH0.tar.gz) = 8041349
Modified: head/biology/hyphy/pkg-plist
==============================================================================
--- head/biology/hyphy/pkg-plist Sat Oct 20 12:14:02 2018 (r482494)
+++ head/biology/hyphy/pkg-plist Sat Oct 20 12:21:15 2018 (r482495)
@@ -237,7 +237,7 @@ lib/hyphy/TemplateBatchFiles/PositiveSelectionLI.bf
lib/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md
lib/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf
lib/hyphy/TemplateBatchFiles/QuickSelectionDetection-MEME-internal.bf
-lib/hyphy/TemplateBatchFiles/QuickSelectionDetection.bf
+lib/hyphy/TemplateBatchFiles/Deprecated/QuickSelectionDetection.bf
lib/hyphy/TemplateBatchFiles/QuickSelectionDetectionMF.bf
lib/hyphy/TemplateBatchFiles/RateClassCounter.bf
lib/hyphy/TemplateBatchFiles/ReduceDataSetMatrix.bf
@@ -267,6 +267,8 @@ lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-S
lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
lib/hyphy/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
lib/hyphy/TemplateBatchFiles/SelectionAnalyses/Simulators/BUSTED.bf
+lib/hyphy/TemplateBatchFiles/SelectionAnalyses/Simulators/FADE.bf
+lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL-NS.bf
lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
@@ -504,6 +506,7 @@ lib/hyphy/TemplateBatchFiles/libv3/models/rate_variati
lib/hyphy/TemplateBatchFiles/libv3/stats.bf
lib/hyphy/TemplateBatchFiles/libv3/tasks/alignments.bf
lib/hyphy/TemplateBatchFiles/libv3/tasks/ancestral.bf
+lib/hyphy/TemplateBatchFiles/libv3/tasks/bayesgraph.ibf
lib/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf
lib/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf
lib/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf
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