From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: (qmail 67260 invoked by alias); 27 Jan 2016 09:06:09 -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 67242 invoked by uid 89); 27 Jan 2016 09:06:08 -0000 Authentication-Results: sourceware.org; auth=none X-Virus-Found: No X-Spam-SWARE-Status: No, score=-1.9 required=5.0 tests=AWL,BAYES_00,FREEMAIL_FROM,RCVD_IN_DNSWL_LOW,SPF_PASS autolearn=ham version=3.3.2 spammy=Hx-languages-length:1321, VERY, HContent-Transfer-Encoding:8bit X-HELO: mail-wm0-f54.google.com Received: from mail-wm0-f54.google.com (HELO mail-wm0-f54.google.com) (74.125.82.54) by sourceware.org (qpsmtpd/0.93/v0.84-503-g423c35a) with (AES128-GCM-SHA256 encrypted) ESMTPS; Wed, 27 Jan 2016 09:06:07 +0000 Received: by mail-wm0-f54.google.com with SMTP id n5so17461422wmn.1 for ; Wed, 27 Jan 2016 01:06:06 -0800 (PST) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:subject:to:references:from:message-id:date :user-agent:mime-version:in-reply-to:content-type :content-transfer-encoding; bh=4eho05oczjC7qQq3pIsH9KjafqeSibkfrMqkIMOjG6o=; b=epIMjQb4Z7RQeL3vsZceL3nAk5Qaoxshj/xHs0ePx36WUWkMk9rdbdhQJpEUkCW0pm edF4Zc9cGKngg3LLTniKXDGbMb1GQtd84b8YIyjQNheITkp7E0DHglTPB8BPfk4AN0zW bGeYT5cgcjy14vTKX4jahhFkJmyXsCFdgyEX9upf5A3pxQZq9DmVl7XVft38T85Z+ck7 i2JmkhPCif4LWhw7Lqf3OPV/iWXM11rC8jrfajiwi+lTefQSOPL2cLpPsj8EEwMZAJcZ upgE8rAEwTxUc4PXiFYU9/5vzD16L4e1NDdiZdYCToTiKI+DX0lhirGbhk8mitYYxgBT ysUQ== X-Gm-Message-State: AG10YORIplBUeAAwtfMdLyuTB2ow4jAATk/VBFQtp34UwqPhDNeES6gtQipfNX8tinPkFw== X-Received: by 10.194.117.134 with SMTP id ke6mr31709433wjb.94.1453885563993; Wed, 27 Jan 2016 01:06:03 -0800 (PST) Received: from [172.21.188.188] ([62.154.173.198]) by smtp.googlemail.com with ESMTPSA id e8sm1456063wjy.43.2016.01.27.01.06.03 for (version=TLSv1/SSLv3 cipher=OTHER); Wed, 27 Jan 2016 01:06:03 -0800 (PST) Subject: Re: bcftools error running Make after installing update 2.4.1.1 to Cygwin64 To: cygwin@cygwin.com References: From: Marco Atzeri Message-ID: <56A88876.1040808@gmail.com> Date: Wed, 27 Jan 2016 11:46:00 -0000 User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:38.0) Gecko/20100101 Thunderbird/38.5.1 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit X-IsSubscribed: yes X-SW-Source: 2016-01/txt/msg00381.txt.bz2 On 27/01/2016 05:53, Robert May wrote: > I have had another look at Makefile and I changed c to gnu in this line 40 -std=gnu99 > CFLAGS = -g -Wall -Wc++-compat -O2 -std=gnu99 > > I had also removed -rdynamic in line 185 so it now reads > $(CC) $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS) > > and ran make again > > Like sametools it has many warning essages about ‘expl’, ‘alloca’, ‘fileno’, ‘char’, this last one being the most prominent and ends with > > prob1.o: In function `mc_cal_y': > /usr/local/bin/bcftools-1.3/prob1.c:320: undefined reference to `expl' > /usr/local/bin/bcftools-1.3/prob1.c:320:(.text+0x1842): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `expl' > collect2: error: ld returned 1 exit status > Makefile:185: recipe for target 'bcftools' failed > make: *** [bcftools] Error 1 > > this is the same error message as in samtools collect2: error: ld returned 1 exit status > but a different culprit prob1.o: In function `mc_cal_y': > > > Bob May Bob, it seems you are missing some includes fileno is defined in /usr/include/stdio.h alloca in /usr/include/alloca.h expl is not available so use exp are workaround That char is not defined seems VERY VERY strange -- 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