From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 3B737138A3F for ; Fri, 3 Apr 2015 15:31:30 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id B811BE09E6; Fri, 3 Apr 2015 15:31:29 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 345D4E09E6 for ; Fri, 3 Apr 2015 15:31:29 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 67AAC3408CF for ; Fri, 3 Apr 2015 15:31:28 +0000 (UTC) Received: by oystercatcher.gentoo.org (Postfix, from userid 2276) id F37AA15215; Fri, 3 Apr 2015 15:31:25 +0000 (UTC) From: "Andreas HAttel (dilfridge)" To: gentoo-commits@lists.gentoo.org Reply-To: gentoo-dev@lists.gentoo.org, dilfridge@gentoo.org Subject: [gentoo-commits] gentoo-x86 commit in sci-biology/vcftools/files: vcftools-0.1.12b-buildsystem.patch X-VCS-Repository: gentoo-x86 X-VCS-Files: vcftools-0.1.12b-buildsystem.patch X-VCS-Directories: sci-biology/vcftools/files X-VCS-Committer: dilfridge X-VCS-Committer-Name: Andreas HAttel Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit Message-Id: <20150403153125.F37AA15215@oystercatcher.gentoo.org> Date: Fri, 3 Apr 2015 15:31:25 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: e09a7f1a-1441-4480-9878-9deef2739a7e X-Archives-Hash: 5af72feb690ab9159342823587aa4990 dilfridge 15/04/03 15:31:25 Added: vcftools-0.1.12b-buildsystem.patch Log: Version bump, fixing bug 545304 (Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key 0B08240A96F66571) Revision Changes Path 1.1 sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch?rev=1.1&content-type=text/plain Index: vcftools-0.1.12b-buildsystem.patch =================================================================== diff -ur vcftools_0.1.12b.orig/cpp/Makefile vcftools_0.1.12b/cpp/Makefile --- vcftools_0.1.12b.orig/cpp/Makefile 2014-08-01 21:11:22.000000000 +0200 +++ vcftools_0.1.12b/cpp/Makefile 2015-04-03 17:24:38.830781049 +0200 @@ -3,8 +3,8 @@ # ($Revision: 1.1 $) # Compiler -CC = gcc -CPP = g++ +CC ?= gcc +CPP ?= g++ # Output executable EXECUTABLE = vcftools # Flag used to turn on compilation of PCA routines @@ -12,9 +12,9 @@ VCFTOOLS_PCA = 0 endif # Compiler flags -CFLAGS = -O2 -m64 +CFLAGS ?= -O2 -m64 #CFLAGS = -Wall -O2 -pg -m64 -CPPFLAGS = -O2 -D_FILE_OFFSET_BITS=64 +CPPFLAGS ?= -O2 -D_FILE_OFFSET_BITS=64 #CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64 # Included libraries (zlib) LIB = -lz @@ -29,13 +29,13 @@ # Define flag for PCA routine compilation CPPFLAGS += -DVCFTOOLS_PCA # Add LAPACK library - LIB += -llapack + LIB += `$(PKG_CONFIG) --libs lapack` # Add PCA source code OBJS+= dgeev.o endif vcftools: $(OBJS) - $(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB) + $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(OBJS) -o vcftools $(LIB) ifdef BINDIR cp $(CURDIR)/$@ $(BINDIR)/$@ endif @@ -47,8 +47,8 @@ -include $(OBJS:.o=.d) %.o: %.cpp - $(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o - $(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d + $(CXX) -c $(CXXFLAGS) $(CPPFLAGS) $*.cpp -o $*.o + $(CXX) -MM $(CXXFLAGS) $(CPPFLAGS) $*.cpp > $*.d # remove compilation products clean: