From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: (qmail 12905 invoked by alias); 25 Jan 2016 21:30:39 -0000 Mailing-List: contact cygwin-help@cygwin.com; run by ezmlm Precedence: bulk List-Id: List-Subscribe: List-Archive: List-Post: List-Help: , Sender: cygwin-owner@cygwin.com Mail-Followup-To: cygwin@cygwin.com Received: (qmail 12887 invoked by uid 89); 25 Jan 2016 21:30:38 -0000 Authentication-Results: sourceware.org; auth=none X-Virus-Found: No X-Spam-SWARE-Status: No, score=-0.8 required=5.0 tests=BAYES_00,FREEMAIL_FROM,KAM_COUK,RP_MATCHES_RCVD,SPF_PASS autolearn=no version=3.3.2 spammy=pride, Hx-spam-relays-external:sk:smtp-ou, H*RU:sk:smtp-ou, HX-HELO:sk:smtp-ou X-HELO: smtp-out-11.tiscali.co.uk Received: from smtp-out-11.tiscali.co.uk (HELO smtp-out-11.tiscali.co.uk) (62.24.139.98) by sourceware.org (qpsmtpd/0.93/v0.84-503-g423c35a) with ESMTP; Mon, 25 Jan 2016 21:30:37 +0000 Received: from [192.168.1.3] ([92.3.193.39]) by smtp.talktalk.net with SMTP id NoiTad2e07DWMNoiYadSTG; Mon, 25 Jan 2016 21:30:34 +0000 Subject: Re: bcftools error running Make after installing update 2.4.1.1 to Cygwin64 To: cygwin@cygwin.com References: From: David Stacey Message-ID: <56A693F5.7070000@tiscali.co.uk> Date: Tue, 26 Jan 2016 17:23:00 -0000 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:38.0) Gecko/20100101 Thunderbird/38.5.0 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit X-CMAE-Envelope: MS4wfMcyH8qk0bzSgBLieGS0p9OPM9okhhKffovvAZ+jj8kX6/fUhtSyRCWBP+uPZx+4JeWP/d9lzEAfTUP1XfwV7y4+GgNY3rLB/ZkoMfZnjhlD4M0ttrje 2OxMNLvC2uDnq54gUraYJgNKARy0C4zduUZdplL4I+naXUbpT5n0KArm X-IsSubscribed: yes X-SW-Source: 2016-01/txt/msg00362.txt.bz2 On 25/01/16 21:00, Robert May wrote: > many warnings are given in the following text - see end for error message > > echo '#define BCFTOOLS_VERSION "1.3"'> version.h > gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o main.o main.c > gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o vcfindex.o vcfindex.c > vcfindex.c: In function ‘main_vcfindex’: > vcfindex.c:209:9: warning: implicit declaration of function ‘alloca’ [-Wimplicit-function-declaration] > char*idx_fname = (char*)alloca(strlen(fname) + 5); > ^ > vcfindex.c:209:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > char*idx_fname = (char*)alloca(strlen(fname) + 5); These warnings can be generated for a number of reasons. One is that the source code you are attempting to compile pre-dates this version of gcc. Another reason is that you are somehow using a combination of compiler switches that were never expected. A third reason is that the source code simply isn't well written, but the majority of Open Source contributors take great pride in their work. In your case, it could be the compiler switches - see below. > gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o vcfcnv.o vcfcnv.c > vcfcnv.c: In function ‘norm_prob’: > vcfcnv.c:602:93: error: ‘M_PI’ undeclared (first use in this function) > return exp(-(baf-param->mean)*(baf-param->mean)*0.5/param->dev2) / param->norm / sqrt(2*M_PI*param->dev2); > ^ > vcfcnv.c:602:93: note: each undeclared identifier is reported only once for each function it appears in > vcfcnv.c: In function ‘main_vcfcnv’: > vcfcnv.c:1349:9: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration] > if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; > ^ > vcfcnv.c: In function ‘norm_prob’: > vcfcnv.c:603:1: warning: control reaches end of non-void function [-Wreturn-type] > } > ^ This looks like expected behaviour to me. Specifying '-std=c99' defines a __STRICT_ANSI__ macro, which in turn means that mathematical constants like M_PI are not defined. Using '-std=gnu99' instead should work. You may also find that this more relaxed compiler setting doesn't generate so many warnings. Dave. -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple