From nobody Sun Mar 20 15:29:02 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 AB1E91A21818; Sun, 20 Mar 2022 15:29:02 +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 4KM1qy4CVRz3jgZ; Sun, 20 Mar 2022 15:29:02 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1647790142; 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=/Daqc3ZUFDHEVEInA9NMdOTU7sVfwE3nL+2uYNzNEYE=; b=NaYbjK/KDhkB2Zz5Hjsv9lDAwPoMaI1zTk7qvTXaQrqE8rMqO9ZnuzVQvW7ScDfIhrKdic R20Y38MmehgdmWTpSNViaSz0UtkRusvy5IxZi/iUEx7QRg0pSTw3rj8YreTcauiPcgUZ7n TPrYosWOrKOW72WjSNpcbeuA15xlHd/E5ZvYFq2UXEDIZNJpSGLuyfU1qGDFyaXFlbQpbw iWlsz4p5AZj2wva59C1QjeNIcGKxzseUKk3vFT1r9Zd1c8W4zHL9B2Qi7k0+IjgYjZOrks n5dOes4K6WxPrURZh6x/ItVN0Fn/LsCSG28JDXvt+Mc+naLVM4gscmIBTyu1FQ== 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 6C8C51B32; Sun, 20 Mar 2022 15:29:02 +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 22KFT2ao040684; Sun, 20 Mar 2022 15:29:02 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 22KFT2gm040683; Sun, 20 Mar 2022 15:29:02 GMT (envelope-from git) Date: Sun, 20 Mar 2022 15:29:02 GMT Message-Id: <202203201529.22KFT2gm040683@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 0297052e221a - main - biology/bolt-lmm: Update to 2.3.6 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: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 0297052e221a1c1e754fa6d10380a527985f4cf5 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1647790142; 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=/Daqc3ZUFDHEVEInA9NMdOTU7sVfwE3nL+2uYNzNEYE=; b=U2OdY6/2K1l2C83fYJm1L09E6EWqozX9/eGbFuXHEz/atjQLCSxoFHmzzWijCjETq7q04m AVK787Mlt7VKs3z/XjeS2mxDGrki5+S+F0hFFRX7h6YixXAj3BkGQ/Jlgpnlca+r/iYO84 rxYRnabPVo2MYnkNcw34667GbfTacbGKj4T6pN4cFAb/Qiczl7w2jmkK7VtppBMzGIhGcY KQs5V2kIoxPLzk+smotLmUTEE7Z6kMN46GOcFlJ6jSzFGklOLV3h8X8+d1wSMqk7UMzsWc 4ftsOCh2UJ44llhVrGrUk+eEBo4YAUlDzldj837zSLxY1wvkGfFq1OZdBrYQGg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1647790142; a=rsa-sha256; cv=none; b=qd+XTZinOjVIkvYctt3mu2Fp6ftJrtj6tHP/caXktw7mkugb0JAWY/VOZ6gVTeAlPPEncE xQfDRclDuUp+j6eDkS6bSE1Z2OkPT2ecTMb4C8Km1CQM6g+WrhgkqE1X9kYRyEg45ReZEi QS2qv/YKhP9azjrq8l5iSXvUigau41oNU7uUC1ELD0S66nk54+nXFUo5bcCNDa8CAgoKas +YOeIXQuINxBzuCZyRo6mq3cpg9LjC7Hgi5PePBH1Kqhsy2E2WUj19TPuFoCB5Kp8C9Kf9 KdSieziWq1PKvO/TgVyK8Ma++x2iY2tGpx3AR90vL9Kd9GQDidYvwYMQ18VwZw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=0297052e221a1c1e754fa6d10380a527985f4cf5 commit 0297052e221a1c1e754fa6d10380a527985f4cf5 Author: Jason W. Bacon AuthorDate: 2022-03-20 15:23:35 +0000 Commit: Jason W. Bacon CommitDate: 2022-03-20 15:29:01 +0000 biology/bolt-lmm: Update to 2.3.6 Changes: https://alkesgroup.broadinstitute.org/BOLT-LMM/\ BOLT-LMM_manual.html#x1-60002.1 Also fixed build on aarch64: Replaced non-portable _mm_malloc() with aligned_alloc() Reported by: pkg-fallout --- biology/bolt-lmm/Makefile | 9 +++------ biology/bolt-lmm/distinfo | 6 +++--- biology/bolt-lmm/files/patch-src_MemoryUtils.cpp | 12 ++++++++++++ biology/bolt-lmm/files/patch-src_MemoryUtils.hpp | 12 ++++++++++++ 4 files changed, 30 insertions(+), 9 deletions(-) diff --git a/biology/bolt-lmm/Makefile b/biology/bolt-lmm/Makefile index 7302e3ef897b..a1f1d09f21eb 100644 --- a/biology/bolt-lmm/Makefile +++ b/biology/bolt-lmm/Makefile @@ -1,6 +1,5 @@ PORTNAME= bolt-lmm -DISTVERSION= 2.3.4 -PORTREVISION= 4 +DISTVERSION= 2.3.6 CATEGORIES= biology MASTER_SITES= https://data.broadinstitute.org/alkesgroup/BOLT-LMM/downloads/ DISTNAME= BOLT-LMM_v${PORTVERSION} @@ -15,9 +14,7 @@ LIB_DEPENDS= libnlopt.so:math/nlopt \ libopenblas.so:math/openblas \ libboost_program_options.so:devel/boost-libs -# gcc-c++11-lib needed to link with boost. Also requires compiler:openmp, but -# both merely add a GCC requirement. -USES= compiler:gcc-c++11-lib gmake +USES= gmake BUILD_WRKSRC= ${WRKDIR}/${DISTNAME}/src INSTALL_WRKSRC= ${WRKDIR}/${DISTNAME}/src @@ -32,7 +29,7 @@ MAKE_ARGS= BOOST_INSTALL_DIR=${LOCALBASE} \ GLIBC_STATIC_DIR=/usr/lib \ SSEFLAGS="" \ MEMCPY="" \ - LLAPACK="-lopenblas -lgfortran" + LLAPACK="-lopenblas" CONFLICTS_INSTALL= rubygem-bolt # bin/bolt diff --git a/biology/bolt-lmm/distinfo b/biology/bolt-lmm/distinfo index 618a36d60050..4711694315b8 100644 --- a/biology/bolt-lmm/distinfo +++ b/biology/bolt-lmm/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1565528176 -SHA256 (BOLT-LMM_v2.3.4.tar.gz) = 2477faff5028ff8fee5d8f4e6b0cab6d0752b268fd508fe64530a66807d9b0c0 -SIZE (BOLT-LMM_v2.3.4.tar.gz) = 335128004 +TIMESTAMP = 1647782880 +SHA256 (BOLT-LMM_v2.3.6.tar.gz) = bc82a5166b3d2d480bcda1f4455c29e1018db733706d28c35d8bf8de7e1e85d5 +SIZE (BOLT-LMM_v2.3.6.tar.gz) = 335131602 diff --git a/biology/bolt-lmm/files/patch-src_MemoryUtils.cpp b/biology/bolt-lmm/files/patch-src_MemoryUtils.cpp new file mode 100644 index 000000000000..e6a2f20061f9 --- /dev/null +++ b/biology/bolt-lmm/files/patch-src_MemoryUtils.cpp @@ -0,0 +1,12 @@ +--- src/MemoryUtils.cpp.orig 2022-03-20 14:01:47 UTC ++++ src/MemoryUtils.cpp +@@ -26,7 +26,8 @@ void *ALIGNED_MALLOC(uint64 size) { + #ifdef USE_MKL_MALLOC + void *p = mkl_malloc(size, MEM_ALIGNMENT); + #else +- void *p = _mm_malloc(size, MEM_ALIGNMENT); ++ //void *p = _mm_malloc(size, MEM_ALIGNMENT); ++ void *p = aligned_alloc(MEM_ALIGNMENT, size); + #endif + // TODO: change to assert() or dispense with altogether and change ALIGNED_MALLOC to macro? + if (p == NULL) { diff --git a/biology/bolt-lmm/files/patch-src_MemoryUtils.hpp b/biology/bolt-lmm/files/patch-src_MemoryUtils.hpp new file mode 100644 index 000000000000..a9ccbd3d78e7 --- /dev/null +++ b/biology/bolt-lmm/files/patch-src_MemoryUtils.hpp @@ -0,0 +1,12 @@ +--- src/MemoryUtils.hpp.orig 2022-03-20 13:40:42 UTC ++++ src/MemoryUtils.hpp +@@ -31,8 +31,7 @@ void *ALIGNED_MALLOC(uint64 size); + #include + #define ALIGNED_FREE mkl_free + #else +-#include +-#define ALIGNED_FREE _mm_free ++#define ALIGNED_FREE free + #endif + + #define ALIGNED_MALLOC_DOUBLES(numDoubles) (double *) ALIGNED_MALLOC((numDoubles)*sizeof(double))