Received: by mail.netbsd.org (Postfix, from userid 605) id 2CFA084D7A; Tue, 22 May 2018 21:37:31 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id 9A8A884D36 for ; Tue, 22 May 2018 21:37:30 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([127.0.0.1]) by localhost (mail.netbsd.org [127.0.0.1]) (amavisd-new, port 10025) with ESMTP id xKviRGfJPmaI for ; Tue, 22 May 2018 21:37:30 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.NetBSD.org [IPv6:2001:470:a085:999:28c:faff:fe03:5984]) by mail.netbsd.org (Postfix) with ESMTP id 1111284D2C for ; Tue, 22 May 2018 21:37:30 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 074B8FBEB; Tue, 22 May 2018 21:37:30 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1527025050288720" MIME-Version: 1.0 Date: Tue, 22 May 2018 21:37:30 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/ncbi-blast+ To: pkgsrc-changes@NetBSD.org Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20180522213730.074B8FBEB@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: pkgsrc-changes.NetBSD.org Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1527025050288720 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Tue May 22 21:37:29 UTC 2018 Modified Files: pkgsrc/biology/ncbi-blast+: Makefile distinfo pkgsrc/biology/ncbi-blast+/patches: patch-src_build-system_helpers_Makefile.run__with__lock.app Log Message: biology/ncbi-blast+: Respect env to support PKGSRC_USE_RELRO Fix a previous patch that hard-coded relro support by patching in pkgsrc CFLAGS, CXXFLAGS, and LDFLAGS instead. OK wiz@ To generate a diff of this commit: cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/ncbi-blast+/Makefile \ pkgsrc/biology/ncbi-blast+/distinfo cvs rdiff -u -r1.1 -r1.2 \ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1527025050288720 Content-Disposition: inline Content-Length: 3531 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/ncbi-blast+/Makefile diff -u pkgsrc/biology/ncbi-blast+/Makefile:1.1 pkgsrc/biology/ncbi-blast+/Makefile:1.2 --- pkgsrc/biology/ncbi-blast+/Makefile:1.1 Fri Apr 27 20:28:28 2018 +++ pkgsrc/biology/ncbi-blast+/Makefile Tue May 22 21:37:29 2018 @@ -1,7 +1,8 @@ -# $NetBSD: Makefile,v 1.1 2018/04/27 20:28:28 bacon Exp $ +# $NetBSD: Makefile,v 1.2 2018/05/22 21:37:29 bacon Exp $ DISTNAME= ncbi-blast-${PV}+-src PKGNAME= ncbi-blast+-${PV} +PKGREVISION= 1 CATEGORIES= biology MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PV}/ Index: pkgsrc/biology/ncbi-blast+/distinfo diff -u pkgsrc/biology/ncbi-blast+/distinfo:1.1 pkgsrc/biology/ncbi-blast+/distinfo:1.2 --- pkgsrc/biology/ncbi-blast+/distinfo:1.1 Fri Apr 27 20:28:28 2018 +++ pkgsrc/biology/ncbi-blast+/distinfo Tue May 22 21:37:29 2018 @@ -1,4 +1,4 @@ -$NetBSD: distinfo,v 1.1 2018/04/27 20:28:28 bacon Exp $ +$NetBSD: distinfo,v 1.2 2018/05/22 21:37:29 bacon Exp $ SHA1 (ncbi-blast-2.7.1+-src.tar.gz) = d04a25f01c386abd8515957a2ce1dabf376743f8 RMD160 (ncbi-blast-2.7.1+-src.tar.gz) = 7277419e16fb215aae4136a16e13bec963b70cbd @@ -9,4 +9,4 @@ SHA1 (patch-src_algo_blast_core_blast__k SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01 SHA1 (patch-src_build-system_cmake_cmake-configure) = 7b9a10447b1dd665200ee73a2180b3210f586b97 SHA1 (patch-src_build-system_configure) = 90becd948f8aca87fd68081e689bdc8c49b419c6 -SHA1 (patch-src_build-system_helpers_Makefile.run__with__lock.app) = 0fb99ac4e582938fd47e66c146da71695f009b98 +SHA1 (patch-src_build-system_helpers_Makefile.run__with__lock.app) = d69b9e349646c970c3b296707f917defbe39cccd Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app diff -u pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app:1.1 pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app:1.2 --- pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app:1.1 Fri Apr 27 20:28:28 2018 +++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app Tue May 22 21:37:29 2018 @@ -1,9 +1,9 @@ -$NetBSD: patch-src_build-system_helpers_Makefile.run__with__lock.app,v 1.1 2018/04/27 20:28:28 bacon Exp $ +$NetBSD: patch-src_build-system_helpers_Makefile.run__with__lock.app,v 1.2 2018/05/22 21:37:29 bacon Exp $ # Missing RELRO for this one binary # https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=820959 ---- src/build-system/helpers/Makefile.run_with_lock.app.orig 2018-04-27 16:21:07.000000000 +0000 +--- src/build-system/helpers/Makefile.run_with_lock.app.orig 2016-02-23 17:06:47.000000000 +0000 +++ src/build-system/helpers/Makefile.run_with_lock.app @@ -6,9 +6,9 @@ CC = $(CC_FOR_BUILD) CC_WRAPPER = @@ -12,9 +12,9 @@ $NetBSD: patch-src_build-system_helpers_ -CFLAGS = $(CFLAGS_FOR_BUILD) -CPPFLAGS = $(CPPFLAGS_FOR_BUILD) -LDFLAGS = $(LDFLAGS_FOR_BUILD) -+CFLAGS = $(CFLAGS_FOR_BUILD) -Wl,-z,relro,-z,now -+CPPFLAGS = $(CPPFLAGS_FOR_BUILD) -Wl,-z,relro,-z,now -+LDFLAGS = $(LDFLAGS_FOR_BUILD) -Wl,-z,relro,-z,now ++CFLAGS := $(CFLAGS_FOR_BUILD) $(CFLAGS) ++CPPFLAGS := $(CPPFLAGS_FOR_BUILD) $(CPPFLAGS) ++LDFLAGS := $(LDFLAGS_FOR_BUILD) $(LDFLAGS) LIBS = $(C_LIBS) LINK = $(CC) LINK_WRAPPER = --_----------=_1527025050288720--