From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: (qmail 105149 invoked by alias); 27 Jan 2016 11:23:49 -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 105135 invoked by uid 89); 27 Jan 2016 11:23:48 -0000 Authentication-Results: sourceware.org; auth=none X-Virus-Found: No X-Spam-SWARE-Status: No, score=-0.8 required=5.0 tests=AWL,BAYES_00,FREEMAIL_FROM,LIKELY_SPAM_SUBJECT,RCVD_IN_DNSWL_LOW,SPF_PASS autolearn=no version=3.3.2 spammy=sk:tpibob@, sk:tpibob, tpibobgmailcom, tpibob@gmail.com X-HELO: mail-pf0-f169.google.com Received: from mail-pf0-f169.google.com (HELO mail-pf0-f169.google.com) (209.85.192.169) by sourceware.org (qpsmtpd/0.93/v0.84-503-g423c35a) with (AES128-GCM-SHA256 encrypted) ESMTPS; Wed, 27 Jan 2016 11:23:47 +0000 Received: by mail-pf0-f169.google.com with SMTP id n128so3436373pfn.3 for ; Wed, 27 Jan 2016 03:23:47 -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 :in-reply-to:references:content-type:content-transfer-encoding :mime-version; bh=pgdLFKMOn2aY4s5jluxCoegGSMeQjDzh0Bw2vjK7tEs=; b=A314AliiQkUhEwW4VoZxN/4JRVQdeDtMzXMqcupwhMyUoIPUdYWLBi68oRR9+Q8w2r qnbM0TLAdWeqj81xsotHGnDi7K/tbCHLKMxWjBPBwO1TROuwC2gnjdK9B7pqOulmmwHo 8gVtWi5ZuDPVbs0KWgTwd2OlgB+p76/K03UsiM0syDyHD+EtOQmvpSU0lsHpxF3cyM3S 400yTvSBRwtPHxrfrS11c0gwxNKLus2zaR/VZnnNsn0N5U1hvBEOK6aIjXrJB0oJz6Cl nNu933muvAUaPLg3YJt03TUVYRgcYrna2k076fuUPQEYcQ75Mw4v35L3rdq0BGNJFiGJ R0Gw== X-Gm-Message-State: AG10YORGTfAVMS8h0z/dOPZJFqWkdZEHBHg2WkgugRsJS8/r4tV/MkR56BM+75UPma//Cw== X-Received: by 10.98.19.214 with SMTP id 83mr41743731pft.22.1453893825725; Wed, 27 Jan 2016 03:23:45 -0800 (PST) Received: from mail.hotmail.com (col004-wss1s1.hotmail.com. [157.56.23.8]) by smtp.gmail.com with ESMTPSA id e1sm8433012pas.1.2016.01.27.03.23.45 for (version=TLSv1/SSLv3 cipher=OTHER); Wed, 27 Jan 2016 03:23:45 -0800 (PST) Received: from BAY175-W36 ([157.56.23.7]) by COL004-WSS1S1.hotmail.com over TLS secured channel with Microsoft SMTPSVC(7.5.7601.23008); Wed, 27 Jan 2016 03:23:44 -0800 X-TMN: [5VYhYQHO1ocmTPnBDdAkHVJ5nvwp+o/w] Message-ID: From: Robert May To: "cygwin@cygwin.com" Subject: FW: Re Samtools error after installing cygwin64 4.3.1.1 Date: Wed, 27 Jan 2016 12:41:00 -0000 In-Reply-To: References: , Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-SW-Source: 2016-01/txt/msg00384.txt.bz2 MarcoYes got samtools configure make install=20 samtools=20 =3D samtools index appears What I did line 26 added -std=3Dgnu99 line 31 added -D_CURSES_LIB=3D1 -Dexpl=3Dexp -Dlogl=3Dlogline 87 removed -r= dynamic am about to try the program out Bob =A0Bob May DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surn= ame and ISOGG=A0YTree > From: tpibob@gmail.com > To: cygwin@cygwin.com > Subject: Re error after installing cygwin64 4.3.1.1 > Date: Wed, 27 Jan 2016 14:24:21 +1000 >=20 > 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 >=20 > 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_r= mdupse.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 b= edcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_spli= t.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quick= check.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 truncat= ed 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 truncat= ed 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 >=20 > this is the culprit I believe=20 > errmod.o: In function `cal_coef': > regards > Bob >=20 > =A0Bob May > DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Su= rname and ISOGG=A0YTree=20=09=09=20=09=20=20=20=09=09=20=20 =20=09=09=20=09=20=20=20=09=09=20=20=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