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=ooDAOOx565VODwgK
	RDIHkYVdGa+RrUDRarq3SnYrmg00HpyZ79tN1LD9Mm+6/XWc3fBbNogr3/tp5gBx
	OYmnNP91TkdAvLFdQGx9ZPdVYB8Dl25ml7CGjyDSBidLFo+uD7LGrEBNIDLaJv0F
	J36+L8CmjVOQb0qXC4KmZAsNCUo=
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=LUao4k+w9m+UsWB/bN06bN
	fuXe0=; b=LYFkWm4khTx2QYvQEn0fB/HgZiqqLN1HEEljFkvFiAlepaoHzySTUG
	gZtHUem0Qyll1xjLramYQLo8sxbP7AGSqJyrAESr7UDu6glUXGRgydMcwlQLIAx1
	6URbufVJDh7yKog5/xxYKktVk08cjrEVKCQtVlswEuc7EEBhtOBxw=
Mailing-List:	contact cygwin-help AT cygwin DOT com; run by ezmlm
List-Id:	<cygwin.cygwin.com>
List-Subscribe:	<mailto:cygwin-subscribe AT cygwin DOT com>
List-Archive:	<http://sourceware.org/ml/cygwin/>
List-Post:	<mailto:cygwin AT cygwin DOT com>
List-Help:	<mailto:cygwin-help AT cygwin DOT com>, <http://sourceware.org/ml/#faqs>
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=-1.6 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:1742
X-HELO:	mail-wm0-f53.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=CvzOMExD7mwNVVDQNp/HMj+RKKFOs94xRFwD0FmC13A=; b=CBevTaENtvPHg1quTHLVaeCbLv3PJGNDTezrwtoxUfB9DF1ZzV9tl4loox44Jp0FNh Dc4O1U0AiZJLqMj+QlklQUQ0hFtAKJ7EY1fik5VZ/7QH7ayjj0PDo0PfgabpoCTXBL+e O7E1/ZveSJfv12azRebwBY2U3oEcqxLmE4CSgpwgvVwuy2HLmz7LSelmSr/puoqYHHsX dMQyirGgqpt6poDRu/nHXelIrRcEl/QYObpuxQ96uqAYRXHOhe8awthdBYcaB0jng1qD sOPqbWRRrcYdfAb1y2ozH3UJjkKbQ1ma/gK3vI2yqdvGmF7HLrNWdUs3w9y1hW7OR4qJ WtZA==
X-Gm-Message-State:	AG10YORCQQc8WjJXMGrp2qDUYiWvTHK+RULQ0BCMiz4fsa7daJYu9fv6pmDKN7dr8WUgKA==
X-Received:	by 10.194.78.175 with SMTP id c15mr28184492wjx.16.1453884732532; Wed, 27 Jan 2016 00:52:12 -0800 (PST)
Subject:	Re: Re error after installing cygwin64 4.3.1.1
To:	cygwin AT cygwin DOT com
References:	<BAY175-W315899B1CB94BF0A9EDB3CADD90 AT phx DOT gbl>
From:	Marco Atzeri <marco DOT atzeri AT gmail DOT com>
Message-ID:	<56A88537.7000205@gmail.com>
Date:	Wed, 27 Jan 2016 09:52:07 +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:	<BAY175-W315899B1CB94BF0A9EDB3CADD90@phx.gbl>
X-IsSubscribed:	yes

On 27/01/2016 05:24, Robert May wrote:
> Marco
> what I have done is in makefile
> line 26CFLAGS   = -g -Wall -O2   -std=gnu99
> ## added -std=gnu99 above
> line 66
> ALL_LDFLAGS  =  $(HTSLIB_LDFLAGS) $(LDFLAGS)
> ## remove -rdynamic from ALL_LDFLAGS above
>
> and this is the result of the next make run
> Robert AT DESKTOP-14EL82S /usr/local/bin/samtools-1.3
> $ make
> gcc -pthread   -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_rmdupse.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 bedcov.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_quickcheck.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
> errmod.o: In function `cal_coef':
> regards
> Bob
>
>   Bob May

Hi Bob,
as I mentioned expl and logl are not available yet on cygwin.

One workaround with less accuracy is to replace them with exp and log


--
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

- Raw text -