git: 5fa506511af3 - main - biology/gcta: Use bundled version of eigen3

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=5fa506511af383c8b1a2f49f861df31966d32493

commit 5fa506511af383c8b1a2f49f861df31966d32493
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2022-07-06 20:23:30 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2022-07-06 20:40:04 +0000

    biology/gcta: Use bundled version of eigen3
    
    ... in preparation to upgrading math/eigen to 3.4.0.
    
    This version of gcta (1.26.0) doesn't support eigen-3.4.0, and
    it can't be upgraded because latest versions of gcta use
    Intel's closed source MKL library.
    
    PR:             265032
    Suggested by:   tcberner@
    Approved by:    portmgr (interoperability)
---
 biology/gcta/Makefile | 16 +++++++++++-----
 biology/gcta/distinfo |  4 +++-
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/biology/gcta/Makefile b/biology/gcta/Makefile
index 67afd90d9a71..37f0edc6cc84 100644
--- a/biology/gcta/Makefile
+++ b/biology/gcta/Makefile
@@ -2,8 +2,10 @@ PORTNAME=	gcta
 DISTVERSION=	1.26.0
 PORTREVISION=	3
 CATEGORIES=	biology
-MASTER_SITES=	https://cnsgenomics.com/software/gcta/pre_gcta/
-DISTNAME=	${PORTNAME}_${PORTVERSION}_src
+MASTER_SITES=	https://cnsgenomics.com/software/gcta/pre_gcta/:main \
+		https://gitlab.com/libeigen/eigen/-/archive/${EIGEN_VERSION}/:eigen
+DISTFILES=	${PORTNAME}_${DISTVERSION}_src${EXTRACT_SUFX}:main \
+		eigen-${EIGEN_VERSION}.tar.gz:eigen
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Genome-wide Complex Trait Analysis
@@ -13,15 +15,19 @@ LICENSE_FILE=	${WRKSRC}/GNU_General_Public_License_v3.txt
 
 LIB_DEPENDS=	libopenblas.so:math/openblas
 
-USES=		compiler:c++11-lang dos2unix eigen:3 gmake localbase:ldflags zip
+USES=		compiler:c++11-lang dos2unix gmake localbase:ldflags zip
 
-CXXFLAGS+=	-I${LOCALBASE}/include/eigen3 -fopenmp
+CXXFLAGS+=	-I${WRKDIR}/eigen-${EIGEN_VERSION} -fopenmp
 LDFLAGS+=	-lopenblas
 
 INSTALL_TARGET=	install-strip
 PLIST_FILES=	bin/gcta
 
+EIGEN_VERSION=	3.3.9
+
 do-extract:
-	${UNZIP_NATIVE_CMD} -d ${WRKSRC} ${DISTDIR}/${DISTFILES}
+	@${UNZIP_NATIVE_CMD} -d ${WRKSRC} ${DISTDIR}/${PORTNAME}_${DISTVERSION}_src${EXTRACT_SUFX}
+	@cd ${WRKDIR} && \
+		${TAR} xzf ${DISTDIR}/eigen-${EIGEN_VERSION}.tar.gz
 
 .include <bsd.port.mk>
diff --git a/biology/gcta/distinfo b/biology/gcta/distinfo
index 9faabb4559b8..91c72879eac1 100644
--- a/biology/gcta/distinfo
+++ b/biology/gcta/distinfo
@@ -1,3 +1,5 @@
-TIMESTAMP = 1489125670
+TIMESTAMP = 1657137653
 SHA256 (gcta_1.26.0_src.zip) = 554c48f421c93cbaf64b1c300ca507d8e7a56086b5c7d857227fbd4048f42acf
 SIZE (gcta_1.26.0_src.zip) = 198045
+SHA256 (eigen-3.3.9.tar.gz) = 7985975b787340124786f092b3a07d594b2e9cd53bbfe5f3d9b1daee7d55f56f
+SIZE (eigen-3.3.9.tar.gz) = 2142379