From nobody Thu Feb 9 15:35:34 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 4PCLY23q3Nz3pgWv; Thu, 9 Feb 2023 15:35:34 +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 4PCLY22pnhz46TK; Thu, 9 Feb 2023 15:35:34 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1675956934; 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=tIMHcPTEOAwtm9TirSeL0zzAxC4W/rmURfnNshDEhzA=; b=FEf2U2Jdz2cPBMOv8R5GjcvR58/4iQWFWx3OHYRGzB9ENnOFc0MytMc5P1g5oT12Faar4r N9dwPKEqkn5Nt8ymrJZ18wkXfXFqasCF0crhVjM7+lqB9n5x76wGSRisNufWKx7/MHaU6L zfWmIVFK920OvLhxLortUYJJlWxXGGnTQD0tB7SPDpK0oXqSBgtz7J+Gh21fMyiCPo1ux4 1aaMl8e32o1AlQ+IMCCWO+XnRtxttHREvwoLKTh0PIhhQdj0uF5EVYQrfsa8HYLfOnWifd VCjrST6fspYgoACo4U449XuvD9O9n7xqVb7EAc3P0jfXQRRDic6HYrCTwWQlpw== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1675956934; 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=tIMHcPTEOAwtm9TirSeL0zzAxC4W/rmURfnNshDEhzA=; b=is0uzdYS87Bfvv0seAhPhK2D7dm7GMyACg7CKHbSK1v5hsjeUodTv4vIiebEve2z3D0Gxk SP0L8lZovpEMZ40NUOBLEhBPQJO2TgHiNcs37Xg6sLPZUlnYA+cl5SWpcstxmhOQhwDgl7 5qe+ogs1JK9TQ2HMkFdFuP7Bago2BXBloBOBQ0xAbNq8nPOS7e9QiFEgQxuNJmzK+UeDSJ acxMWWI0mSZQ9/mxL7eS/oiQtBA7xVANnJ6jFx7CLf1Y/TsPZve2HxbT7SzURTgEmMux3T 4jg/+TXlWOPytSHAVvUC72DkQrlHGQCcNMun0SI5g69Xyfi7uYI/L22S45pkyQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1675956934; a=rsa-sha256; cv=none; b=I35NOubC/PI1lLUQHUfcI5lCnmPN/y67sa/JctCZGL1cs87vDcIr6t1x+Le335+XKel9ZS oWPnpLL1NhG3AJ0fKDF0za5Rs36hqAezRZQ22pmzEl2TEA2WfI7WbUorHgPKo21WN3otKw Oxbe14KvQDCw+8NMdd3oAN8lxvF/WMGy4zYFjXKDnZ1eNcynJktuP3jemW61EhEMeDLP/6 Ro0+ZFObvAbsZiXB/Fedn0NLHnmy+QqrPhETF6j3J+gZcls3ibCLMALLsFqQUdL7CUX+A2 Wl9H+qQpLW6uwCZyb/H08o7zirdMMJhbMmFb7ty8OvxBNnowy+xEYNjP0Gcphg== 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 4PCLY21ssCzjL8; Thu, 9 Feb 2023 15:35:34 +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 319FZYZf051062; Thu, 9 Feb 2023 15:35:34 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 319FZYs1051061; Thu, 9 Feb 2023 15:35:34 GMT (envelope-from git) Date: Thu, 9 Feb 2023 15:35:34 GMT Message-Id: <202302091535.319FZYs1051061@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: 5fee60fc3c92 - main - biology/vcflib: Update to 1.0.7 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: 5fee60fc3c922a534c2200372385de54590122a9 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=5fee60fc3c922a534c2200372385de54590122a9 commit 5fee60fc3c922a534c2200372385de54590122a9 Author: Jason W. Bacon AuthorDate: 2023-02-09 15:33:16 +0000 Commit: Jason W. Bacon CommitDate: 2023-02-09 15:35:32 +0000 biology/vcflib: Update to 1.0.7 Fixes regression in 1.0.6 Made Zig language support a default off option Zig is experimental and problematic Reported by: portscout --- biology/vcflib/Makefile | 21 +++++++++++++++++---- biology/vcflib/distinfo | 6 +++--- biology/vcflib/pkg-plist | 2 +- 3 files changed, 21 insertions(+), 8 deletions(-) diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile index 76e01dc75cbb..aa44ead39385 100644 --- a/biology/vcflib/Makefile +++ b/biology/vcflib/Makefile @@ -1,7 +1,6 @@ PORTNAME= vcflib DISTVERSIONPREFIX= v -DISTVERSION= 1.0.6 -PORTREVISION= 1 +DISTVERSION= 1.0.7 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -10,8 +9,7 @@ WWW= https://github.com/vcflib/vcflib LICENSE= MIT -BUILD_DEPENDS= zig>0:lang/zig \ - pybind11>=0:devel/pybind11 +BUILD_DEPENDS= pybind11>0:devel/pybind11 LIB_DEPENDS= libhts.so:biology/htslib \ libcurl.so:ftp/curl \ libwfa2.so:biology/wfa2-lib @@ -31,14 +29,29 @@ GH_TUPLE= ekg:fastahack:bb33265:fastahack/contrib/fastahack \ vcflib:tabixpp:v1.1.2:tabixpp/contrib/tabixpp SHEBANG_FILES= scripts/* +# FIXME: Add Zig option + lang/zig dep +OPTIONS_DEFINE= ZIG +OPTIONS_DEFAULT= +OPTIONS_SUB= yes + +ZIG_DESC= Include Zig language support + +ZIG_BUILD_DEPENDS= zig>0:lang/zig + CMAKE_ARGS+= -DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so +ZIG_CMAKE_OFF= -DZIG=OFF # Clang and GCC disable sse2 by default on i386, but it's required for vcflib CFLAGS_i386= -msse2 CONFLICTS_INSTALL= filevercmp libdisorder # include/disorder.h include/filevercmp.h include/pdflib.hpp +.include + post-stage: + ${MV} ${STAGEDIR}${PREFIX}/bin/libvcflib.a ${STAGEDIR}${PREFIX}/lib +.if ${PORT_OPTIONS:MZIG} ${MV} ${STAGEDIR}/usr/lib/libzig.a ${STAGEDIR}${PREFIX}/lib +.endif .include diff --git a/biology/vcflib/distinfo b/biology/vcflib/distinfo index b31324e88085..b8b4cf640ce0 100644 --- a/biology/vcflib/distinfo +++ b/biology/vcflib/distinfo @@ -1,6 +1,6 @@ -TIMESTAMP = 1675089755 -SHA256 (ekg-vcflib-v1.0.6_GH0.tar.gz) = 3598d1a9f6c936c58be6a567f249c1df879a49b57dc5a967b83a7856a16ceeb6 -SIZE (ekg-vcflib-v1.0.6_GH0.tar.gz) = 23545077 +TIMESTAMP = 1675907454 +SHA256 (ekg-vcflib-v1.0.7_GH0.tar.gz) = 37ddf471c5fec2c7fa5d1c2c2e80b3e9d30e401ee3b82156f6ae994652950a38 +SIZE (ekg-vcflib-v1.0.7_GH0.tar.gz) = 23546536 SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760 SHA256 (ekg-filevercmp-df20dcc_GH0.tar.gz) = d34bec614be638e05eb6fa419c936b9e7de58d50b1a096a5ca02aadb7db6b059 diff --git a/biology/vcflib/pkg-plist b/biology/vcflib/pkg-plist index b5b53667909c..297ee6aaa750 100644 --- a/biology/vcflib/pkg-plist +++ b/biology/vcflib/pkg-plist @@ -157,7 +157,7 @@ include/vcf-c-api.h include/vec128int.h include/veclib_types.h lib/libvcflib.a -lib/libzig.a +%%ZIG%%lib/libzig.a lib/pyvcflib%%PYTHON_EXT_SUFFIX%%.so man/man1/abba-baba.1.gz man/man1/bFst.1.gz