From nobody Fri Jul 14 16:12:07 2023 X-Original-To: dev-commits-ports-all@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 4R2c1h17XBz4nFv5; Fri, 14 Jul 2023 16:12:08 +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 4R2c1h0dczz3njM; Fri, 14 Jul 2023 16:12:08 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1689351128; 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=yA11Z+KYRrokR/1lTNvun2r6jbsw1cFK+xXgeEf0+BY=; b=dsPZcBGXRq6ETPrW00AhMQLzZ0IWLyiIB0V2kt9I9xIx7Yif4x1s54Xq7SeumZd+8uWAnk HVvYM1WDN5XbVPa8/3zAtbGj/H1cL0q6OBS70X1vEC3oLGx/QH2UpktPqmG6aiNZSbwJdd jVmgcBp08fyKjuYD3LV93a9t7x5CNkkGA7gZbYJJXsREXT3zmFvk3wD8K+f5eFoSebxf3X IRe+fVCy/zSGTVq6jO5Y/2ec75cXTXGqyFeuXE97JwD75uh3Su3FqVY0uMEz5nG/s4Ljy/ mbIgnJlEnsrrmvse0Clz/N6JjT9shH5HvLE4SxQ9g96Cuh3+Dqu3Q0N2YFb1+g== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1689351128; 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=yA11Z+KYRrokR/1lTNvun2r6jbsw1cFK+xXgeEf0+BY=; b=yB6Z9oexDAEzSLR6fWz4olWpb+Muk9a8m6WGKw58FZ8um+2RxrIgCZ6HxgfZGRSL2MVVMh TbuFp+QfmqnEDrHzEnV+6O/+1BNCB8D7yQHwhkgVqrEaXVTNRmKOWv/SKySY28pLsU5AgT sN7tYWPMABlP2ZajT8jlgvEt5n/6fD33PAozex2eyd0yhshfmPUr9LmYt0U1jZGVuD5f5a a2lE1CjM04WR5LRSdA82zs0M+ZWq4pwB3ZX1Z4mZMNzQb2ZVsI2A8Zppo8EoUwbP98alZe 7g6FaO8xiDCdotsKVxfuBGTl/jUJjqVEDpzGtNagvZ7RH2Qnf+uHWoBUeIK0LQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1689351128; a=rsa-sha256; cv=none; b=N22dvauUipMAmmIvX/CJjkrgIhxUx1nQkfBi0K/TlJXDzJBJ4ZBPBq2c5uyolb4lN+Urc6 HAm+H0mhWm/8fMrwD1BmgQbvK/Uqtax4S9LQIDPqVcLxr6lIpD1gjP1tBSl7gRne95DLpX Y7puA0b+l9Ifx5ujVxw3ihXKXAkG80QLeThKTbp7fAWQaUfEpCjRrqREAAX0DuQmJuZXzz FPyrbJwb8vlULf/64I4K8D634uV+yBBPdd7nhxtB9uzTpJRhgKWvbO9rvQgbEPZKKlg6aC 1vvcYis4UEyFuYXwAHREzw76Ftc4/G0KG/d9bEfZfN8tHNV8KbcfqT6WmenW1A== 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 4R2c1g6phSzPxC; Fri, 14 Jul 2023 16:12:07 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 36EGC7Ru075691; Fri, 14 Jul 2023 16:12:07 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 36EGC77K075690; Fri, 14 Jul 2023 16:12:07 GMT (envelope-from git) Date: Fri, 14 Jul 2023 16:12:07 GMT Message-Id: <202307141612.36EGC77K075690@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: 2b96a02432ae - main - biology/kallisto: Tag only for 64-bit architectures List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@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: 2b96a02432aeacb3a5f477be3477b95f8bd9d2ca Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=2b96a02432aeacb3a5f477be3477b95f8bd9d2ca commit 2b96a02432aeacb3a5f477be3477b95f8bd9d2ca Author: Jason W. Bacon AuthorDate: 2023-07-14 16:10:49 +0000 Commit: Jason W. Bacon CommitDate: 2023-07-14 16:12:06 +0000 biology/kallisto: Tag only for 64-bit architectures Also patch out -march=native Reported by: pkg-fallout --- biology/kallisto/Makefile | 4 ++++ biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt | 11 +++++++++++ 2 files changed, 15 insertions(+) diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index 42715d9abc88..ea7cb1a53596 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -1,6 +1,7 @@ PORTNAME= kallisto DISTVERSIONPREFIX= v DISTVERSION= 0.50.0 +PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= biology @@ -11,6 +12,9 @@ WWW= https://pachterlab.github.io/kallisto/about.html LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt +# Requires a 64-bit processor +ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le riscv64 + LIB_DEPENDS= libhdf5.so:science/hdf5 \ libsz.so:science/libaec \ libhts.so:biology/htslib diff --git a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt new file mode 100644 index 000000000000..c4c22a5e0666 --- /dev/null +++ b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt @@ -0,0 +1,11 @@ +--- ext/bifrost/CMakeLists.txt.orig 2023-07-14 14:27:24 UTC ++++ ext/bifrost/CMakeLists.txt +@@ -30,8 +30,6 @@ if(COMPILATION_ARCH MATCHES "OFF") + message("Disabling native architecture compilation (including AVX2)") + else(COMPILATION_ARCH MATCHES "OFF") + message("Compilation architecture: ${COMPILATION_ARCH}") +- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=${COMPILATION_ARCH}") +- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${COMPILATION_ARCH}") + endif(COMPILATION_ARCH MATCHES "OFF") + + if(ENABLE_AVX2 MATCHES "OFF")