X-Recipient: archive-cygwin AT delorie DOT com DomainKey-Signature: a=rsa-sha1; c=nofws; d=sourceware.org; h=list-id :list-unsubscribe:list-subscribe:list-archive:list-post :list-help:sender:subject:to:references:from:message-id:date :mime-version:in-reply-to:content-type :content-transfer-encoding; q=dns; s=default; b=mXBV/8AzU4UYd0wn hKPJwE9uRm6MyWJHQqWhqYypSd0o4I+VA/CdCUXOCG/32S2fESGZ+7/4itBVH3Lo uMrhq1nF6XmmkiYO///+QE3cfhalhk0TF7NDRHxjNUD+D94XbaQR+paZL7hzEdny Xs4O36vJDgryhQe5rZyryO6fwe8= DKIM-Signature: v=1; a=rsa-sha1; c=relaxed; d=sourceware.org; h=list-id :list-unsubscribe:list-subscribe:list-archive:list-post :list-help:sender:subject:to:references:from:message-id:date :mime-version:in-reply-to:content-type :content-transfer-encoding; s=default; bh=W4VVPJ0em8xt1Dti5kXFT7 AiYGc=; b=cjBtIVazOI17UoZ8aQ5mjgpSUTM5ldIbeMJEipjju4lkA5bpunxEvm oFJ/6gVOmUiso0KZnDdyEf7MoQGTsXVZj6kAGY2YPE8oQ3ZNIAp3lEO1SKSiTV6w FaG1Y85HhikQCv7x3SVJCLLAWSzb6jO1oA2O08txnoBBB7WNnQKwE= Mailing-List: contact cygwin-help AT cygwin DOT com; run by ezmlm List-Id: List-Subscribe: List-Archive: List-Post: List-Help: , Sender: cygwin-owner AT cygwin DOT com Mail-Followup-To: cygwin AT cygwin DOT com Delivered-To: mailing list cygwin AT cygwin DOT com 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 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) Subject: Re: bcftools error running Make after installing update 2.4.1.1 to Cygwin64 To: cygwin AT cygwin DOT com References: From: Marco Atzeri Message-ID: <56A88876.1040808@gmail.com> Date: Wed, 27 Jan 2016 10:05:58 +0100 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 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