Date: Wed, 6 Jul 2022 20:40:06 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 5fa506511af3 - main - biology/gcta: Use bundled version of eigen3 Message-ID: <202207062040.266Ke6uf071704@gitrepo.freebsd.org>
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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
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