From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: (qmail 109078 invoked by alias); 27 Jan 2016 04:53:43 -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 109041 invoked by uid 89); 27 Jan 2016 04:53:41 -0000 Authentication-Results: sourceware.org; auth=none X-Virus-Found: No X-Spam-SWARE-Status: No, score=-1.7 required=5.0 tests=AWL,BAYES_00,FREEMAIL_FROM,RCVD_IN_DNSWL_LOW,SPF_PASS autolearn=ham version=3.3.2 spammy=lpthread, prominent, family, HImportance:Normal X-HELO: mail-pf0-f181.google.com Received: from mail-pf0-f181.google.com (HELO mail-pf0-f181.google.com) (209.85.192.181) by sourceware.org (qpsmtpd/0.93/v0.84-503-g423c35a) with (AES128-GCM-SHA256 encrypted) ESMTPS; Wed, 27 Jan 2016 04:53:12 +0000 Received: by mail-pf0-f181.google.com with SMTP id q63so113948364pfb.1 for ; Tue, 26 Jan 2016 20:53:12 -0800 (PST) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:message-id:from:to:subject:date:importance :content-type:content-transfer-encoding:mime-version; bh=Vz10f6joTQmvR7IsigTj7WrXwjB8LHCkkgEmHn9uaBg=; b=kULC+cSWbYt3rLbJsy0UFd+4WjPFv7sFrNyYGsklxI95IR9hCjASLLWnnPT0zxK0o6 FItNe0tZCYWgwnLg/ksbjia8ixMnolWUIwAanWH5HKSE4i+/hCaBXxekJtyJVZyrAqxO zXLlchBgOXbiT1Qof0rIIh1ZuTzBCUuPD8lmYIqqHmmN3AEgZZcL/4u5LUFoC6amptb5 1iqJDloQ+7E6gc+UTZC3+aERUnnloKaxHlIMVssiUNm4Y1C1eIUPnDJED7Kajes6U36n hhTMb/cbcwjOqzvN+ljqtyMBjE6vcMbymP1tpNqVMdsUf1O5BCHocaPxr03N0YvK9MD3 T8IA== X-Gm-Message-State: AG10YOQnVKrCEJ3Q+vqKmnJARmrzffG4tN+RtGzPGlWgj2CMHllVj8qhpqVMb6vn0y/M7Q== X-Received: by 10.98.44.195 with SMTP id s186mr40443867pfs.0.1453870390202; Tue, 26 Jan 2016 20:53:10 -0800 (PST) Received: from mail.hotmail.com (col004-wss1s3.hotmail.com. [157.56.23.10]) by smtp.gmail.com with ESMTPSA id r12sm5304694pfi.9.2016.01.26.20.53.09 for (version=TLSv1/SSLv3 cipher=OTHER); Tue, 26 Jan 2016 20:53:09 -0800 (PST) Received: from BAY175-W34 ([157.56.23.7]) by COL004-WSS1S3.hotmail.com over TLS secured channel with Microsoft SMTPSVC(7.5.7601.23008); Tue, 26 Jan 2016 20:53:09 -0800 X-TMN: [P4zNMaLjsXWPuMnxH19UzPUhLz1XMhSH] Message-ID: From: Robert May To: "cygwin@cygwin.com" Subject: bcftools error running Make after installing update 2.4.1.1 to Cygwin64 Date: Wed, 27 Jan 2016 08:29:00 -0000 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-SW-Source: 2016-01/txt/msg00375.txt.bz2 I have had another look at Makefile and I changed c to gnu in this line 40 = -std=3Dgnu99 CFLAGS=A0=A0 =3D -g -Wall -Wc++-compat -O2=A0 -std=3Dgnu99 I had also removed -rdynamic in=A0 line 185 so it now reads $(CC)=A0 $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LI= BS) $(LIBS) and ran make again Like sametools it has many warning essages about =91expl=92, =91alloca=92, = =91fileno=92, =91char=92, this last one being the most prominent and ends w= ith=20 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 truncate= d 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': =A0Bob May DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surn= ame and ISOGG=A0YTree=20=09=09=20=09=20=20=20=09=09=20=20 -- 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