From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: (qmail 39468 invoked by alias); 27 Jan 2016 04:24:28 -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 39444 invoked by uid 89); 27 Jan 2016 04:24:26 -0000 Authentication-Results: sourceware.org; auth=none X-Virus-Found: No X-Spam-SWARE-Status: No, score=-1.6 required=5.0 tests=AWL,BAYES_00,FREEMAIL_FROM,RCVD_IN_DNSWL_LOW,SPF_PASS autolearn=ham version=3.3.2 spammy=ldl, culprit, family, HImportance:Normal X-HELO: mail-pf0-f182.google.com Received: from mail-pf0-f182.google.com (HELO mail-pf0-f182.google.com) (209.85.192.182) by sourceware.org (qpsmtpd/0.93/v0.84-503-g423c35a) with (AES128-GCM-SHA256 encrypted) ESMTPS; Wed, 27 Jan 2016 04:24:25 +0000 Received: by mail-pf0-f182.google.com with SMTP id n128so110653938pfn.3 for ; Tue, 26 Jan 2016 20:24:25 -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=0bzMzyihREa70R1yp/C11ojhXiXKP/0ZZxAso1CO+Jw=; b=MIPQm/KyIhUeSxY/3HrU2uz8ljyvIQZ7SOoPdUd3pwniCvK0G9NoTNObiNhThnuDLC M0XDQNcgVVYJyRZDJfNUL4UAi44cfhkyIQchld+ZsJ7JDZ3eMKc2GEelpZ6yUaQ+R/Ig YT18JB9ORXxRINKDAaMOy+3dDuwrK0hNeeE0d/IGOEqwbfNfL1XbiUEcWncTGs/RJl2s J25pUb/vlPghFICy8ZtkmDf0TT60SiS9rwA0Rj633K9iiGERQUmZ3HNZ/4OYCJh06dv5 wq+Okc55lGW6b9hbgFDuuVa1FoO/73VcUIdFAau2Mdejf2+TxvbQ9nvj+j3x1DljpfvU xvGQ== X-Gm-Message-State: AG10YOSBNqkRkbiTqFaTkxXRi3A4WREFIF8q6W/cKcESIzgoguim2RihhortMaYqvEUFnw== X-Received: by 10.98.80.79 with SMTP id e76mr39133521pfb.126.1453868663526; Tue, 26 Jan 2016 20:24:23 -0800 (PST) Received: from mail.hotmail.com (col004-wss1s3.hotmail.com. [157.56.23.10]) by smtp.gmail.com with ESMTPSA id 75sm5116185pfj.20.2016.01.26.20.24.22 for (version=TLSv1/SSLv3 cipher=OTHER); Tue, 26 Jan 2016 20:24:22 -0800 (PST) Received: from BAY175-W31 ([157.56.23.7]) by COL004-WSS1S3.hotmail.com over TLS secured channel with Microsoft SMTPSVC(7.5.7601.23008); Tue, 26 Jan 2016 20:24:22 -0800 X-TMN: [AcdHTTRx52lu7kHWaeAQZbatTPLvRT/E] Message-ID: From: Robert May To: "cygwin@cygwin.com" Subject: Re error after installing cygwin64 4.3.1.1 Date: Wed, 27 Jan 2016 07:21:00 -0000 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-SW-Source: 2016-01/txt/msg00374.txt.bz2 Marco what I have done is in makefile line 26CFLAGS=A0=A0 =3D -g -Wall -O2=A0=A0 -std=3Dgnu99=20 ## added -std=3Dgnu99 above line 66 ALL_LDFLAGS=A0 =3D=A0 $(HTSLIB_LDFLAGS) $(LDFLAGS) ## remove -rdynamic from ALL_LDFLAGS above and this is the result of the next make run Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3 $ make gcc -pthread=A0=A0 -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o= bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmd= upse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o = errmod.o sample.o sam_opts.o cut_target.o phase.o bam2depth.o padding.o bed= cov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.= o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickch= eck.o bam_addrprg.o libbam.a htslib-1.3/libhts.a -lncursesw -lm -lz -ldl errmod.o: In function `cal_coef': /usr/local/bin/samtools-1.3/errmod.c:85: undefined reference to `expl' /usr/local/bin/samtools-1.3/errmod.c:85:(.text+0xc81): relocation truncated= to fit: R_X86_64_PC32 against undefined symbol `expl' /usr/local/bin/samtools-1.3/errmod.c:86: undefined reference to `logl' /usr/local/bin/samtools-1.3/errmod.c:86:(.text+0xca5): relocation truncated= to fit: R_X86_64_PC32 against undefined symbol `logl' collect2: error: ld returned 1 exit status Makefile:140: recipe for target 'samtools' failed make: *** [samtools] Error 1 this is the culprit I believe=20 errmod.o: In function `cal_coef': regards Bob =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