From nobody Thu May 25 09:44:07 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 4QRjn41mg0z4TGkf; Thu, 25 May 2023 09:44:08 +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 4QRjn402rrz3kpl; Thu, 25 May 2023 09:44:08 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1685007848; 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=9/EpEBT5wW145GVvgMfPrSzlpwGHwtNFlXFmAC/31R8=; b=BmN5WRCEQAnVAl11SHSYU2QRhcjSJsnMhk7aX/7H2ntoLZ7YNWD0h3lp3K8a4OyvyxXUyV 1eJNwEyKLThhWO4acSrcgfvAB6EriVDcsH3Hd5vOzLXyYRNQzrxque2CVacZCuER1tkv2w hpAvu5xGw7kE1YWEZISknwUCEp+Zirus/uNvPyf82HjA8NaKX6hcCYI720t9FsgQUg6Hns Px03tYQzJ+iYmTc+D6yUDes1OYjgmg/fBT80hqbbmCt2AsH2xGul3lSKHmMBMp2HFCDqwj Pt4hK0PUdSfNjrty1cbxjbJ4NUE6L8tUdjHbMfzSbU+W1ReAmWLWRCMFna+Ymw== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1685007848; 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=9/EpEBT5wW145GVvgMfPrSzlpwGHwtNFlXFmAC/31R8=; b=jPVMhgS/mku4CW01CowECVgAysj5KRrrAvUWhRwLSOl3/z99k4NlQ7E2i8VO20cPL8aX9Y JMxWxU6aNrWebwYqTcooUlkvgKglaihntm/v7jhrncaORWbb+iT5+sC4PiNhuUoN34xTSv y6FBapu9IV91kZWD0v6s8Yn9ore2PJ77F/lv5jRuCkBw9dpJtYQTNVsrPabVeYmv0/JJHs wkUYYBRT7Qgg01zy7/QZLdYFOcYeTkVE2Uv+2VzeLXEigZSUw/QrMztcb0bEuB3TFMlvgZ h1zKHUMlAxynEdBwEmC52EeMg99h4Hk6esUmqiF73wUFgzD0C+ltGUpcBtxZeQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1685007848; a=rsa-sha256; cv=none; b=OQPhrRxdZyHmKxsSOQmUEXVs4VIXWSMHS0MH+o9HImoJ2/sd3AYqEuqtZ7PonzIELTNyEG iE7XhfXiRgssMI9CTlwf/06ZoNADWo3XyK3F5MjxU8xsbpMJ4cTfE41kuaT3MmhUZQh996 08y2lg9Ek4aC7BeJM+l3AJCpaYqOX6CMNGUkL5EwWWSh69Z+oLDC58ZJLg3OY/gVBXY5s7 bSCS9fiSBvBzaka35w2nE4JhzewSK0zAhkdmnFWWitry11WO1PE7RPXYawAIzUcrmnf6Rd 4XV9nKnhibX2A/dJfZ6W4H5VBzAU/YCt0oYmkMdQYAqHUx0jcjuKYwjFzGgkvA== 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 4QRjn363ftzKnZ; Thu, 25 May 2023 09:44:07 +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 34P9i7dQ001266; Thu, 25 May 2023 09:44:07 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 34P9i7rg001265; Thu, 25 May 2023 09:44:07 GMT (envelope-from git) Date: Thu, 25 May 2023 09:44:07 GMT Message-Id: <202305250944.34P9i7rg001265@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Robert Clausecker Subject: git: 41cce74a9e4c - main - biology/py-pysam: unbundle biology/htslib 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: fuz X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 41cce74a9e4c1727c4120517724059f68f27404f Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by fuz: URL: https://cgit.FreeBSD.org/ports/commit/?id=41cce74a9e4c1727c4120517724059f68f27404f commit 41cce74a9e4c1727c4120517724059f68f27404f Author: Robert Clausecker AuthorDate: 2023-05-24 07:09:35 +0000 Commit: Robert Clausecker CommitDate: 2023-05-25 09:39:33 +0000 biology/py-pysam: unbundle biology/htslib This fixes the build on armv7 by picking up our custom fixed libhts over the bundled unfixed version. The CFLAGS workaround is now no longer required either. Approved by: yuri (maintainer) Differential Revision: https://reviews.freebsd.org/D40251 --- biology/py-pysam/Makefile | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/biology/py-pysam/Makefile b/biology/py-pysam/Makefile index 5cd1b27a49a0..10e1d55b786e 100644 --- a/biology/py-pysam/Makefile +++ b/biology/py-pysam/Makefile @@ -1,5 +1,6 @@ PORTNAME= pysam DISTVERSION= 0.20.0 +PORTREVISION= 1 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,12 +12,15 @@ WWW= https://github.com/pysam-developers/pysam LICENSE= MIT LICENSE_FILE= ${WRKSRC}/COPYING +LIB_DEPENDS= libhts.so:biology/htslib + USES= gmake python:3.6-3.9 USE_PYTHON= autoplist distutils cython cython_run pytest -CFLAGS+= -fPIC # workaround for https://github.com/pysam-developers/pysam/issues/1146 - BINARY_ALIAS= make=${GMAKE} +MAKE_ENV= HTSLIB_MODE=external \ + HTSLIB_LIBRARY_DIR=${LOCALBASE}/lib \ + HTSLIB_INCLUDE_DIR=${LOCALBASE}/include post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysam/lib*${PYTHON_EXT_SUFFIX}.so