From nobody Wed Jul 06 20:40:06 2022 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 7E5A61D0B871; Wed, 6 Jul 2022 20:40:07 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4LdWd31JPNz4Sq5; Wed, 6 Jul 2022 20:40:07 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1657140007; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=/tPrMroLeSsmA/CmOuKDWavtZn1V3pJQhbre6A5DlWI=; b=ts1iseQiq1p3HGRExgaCYQ8pR8uZTHeZL5dVSZP5alD18Q12bebrubx5T39bAfwyFzeJ4V mwFrFQTNlTueLItdmovNCBX8bYRmYbORvHbHwROh9ajjpyWLeEgGgiM34y2Aq8GllzcPF5 DcmAXPzhCDcd2G3g/QTukNRJ6XbrIzXUSeigTagD2K8bJcZgV1H+N5MvghF37aH40g1HrF xZgHA4X/ixV2BUaz/aRHB5syYJZrCjQoMvf8C0xdAbPTsribDylT/syDeS+WxNa6BPVf2m HmUoab6at0pF2jKNjYJbR2INtmHIFYU8iBoJVlDDfTxRyYzg94QOljFa9eQrfw== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 022B3214F8; Wed, 6 Jul 2022 20:40:07 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 266Ke6bO071710; Wed, 6 Jul 2022 20:40:06 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 266Ke6uf071704; Wed, 6 Jul 2022 20:40:06 GMT (envelope-from git) Date: Wed, 6 Jul 2022 20:40:06 GMT Message-Id: <202207062040.266Ke6uf071704@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 5fa506511af3 - main - biology/gcta: Use bundled version of eigen3 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 5fa506511af383c8b1a2f49f861df31966d32493 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1657140007; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=/tPrMroLeSsmA/CmOuKDWavtZn1V3pJQhbre6A5DlWI=; b=rJNmw7b64uQE0nneR1x9X1UyLDPDPSnZKWkJ7lC+7bSOQ605CJ3ewHvlE3Ft5rtRvCfCrp 8OasKgjBRqnXLecb3NN/2rWAXlEVqB4gvTUDso4xS5gXIA5RBH8SUPL1FbEvDTUrcrCcI1 adIMn0uTPhW7b1S+8r7PIYQg0iagADjOW/syhS/gXcauMwnUzqKvziSh3znCu/bJgD9+Gu 07hASO3GJ4G1qDE4dOS5rWqrQX31NWSZKq5WEzz6uEyzeOqYXdWKkOWr7zhhRsSBhMku9e ch/rGQgIyX0zuZ8KsKTrqZEXp6cyxANTMNs8AVZ18P+Z2NC2yG2Q7dROv0b0mg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1657140007; a=rsa-sha256; cv=none; b=Cr5VEKveZiIv7oYR/p48xfrUtdXdeIuHVPqg7Z177IMzz8QOaA5AL9rPSTae+X8MA+8zl1 QawOlgIWY+ET0EWycMSgOR5qtJ8dNnBuwibwJ+6gnpRX7GSOhxQBMN/4VvqRnd2XYUOy+4 LfYHawTgNC4FyDVKRTeZ2BhrK0QLm3KA9mlq/ZCrWNPKvGslG7HeDwvScL7CS1YM8iRcYx aChu6Cv/h4kHVb7J45Lg08d4rsSCJScXivHVAYmUYQD77FE0QA26mJ/7dzdEYcWnSgsxhk EQmqwpUZllOKGUx535k0CG0Gu8LSRtegReApRVrSw6YB2xGxL6/WhcRzU4w2bg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=5fa506511af383c8b1a2f49f861df31966d32493 commit 5fa506511af383c8b1a2f49f861df31966d32493 Author: Yuri Victorovich AuthorDate: 2022-07-06 20:23:30 +0000 Commit: Yuri Victorovich 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 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