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:message-id:from:to:subject:date:content-type
	:content-transfer-encoding:mime-version; q=dns; s=default; b=T+8
	oPCZKGVG7fPfRVn6xsEJvKCHRRAy1geAQU/7ME5jQ0eTPDJZ2s+zVe0NcYAM5AwT
	Glpc2tIZt+BtPPZXvXrYPL225kh3hhAg23KCFVom4MtXaajxAVsr0GvJgN41VYqM
	lJ9Ppc5RMR2XUD69m6jM0xxrRCAVJdxhzFToerhw=
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:message-id:from:to:subject:date:content-type
	:content-transfer-encoding:mime-version; s=default; bh=d7N1QfYq0
	jI16mRSOAZvEE89fu0=; b=pi07p9QXP0N64DixuCgyCqsgSP4WZtN8EV3rr98kL
	NlZdElCuYJrK0tGE3C+EfP5OwS+gkS4+nAyGQU4UQN6sazS6nmqZwp0vJJth58iZ
	IJYTxpsjoI2CDk+9ZVG+pgA0bAZcfQYlISzVG80lavbnTdhgzmS00JRY4xXs9UQU
	bY=
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=ldl, culprit, family, HImportance:Normal
X-HELO:	mail-pf0-f182.google.com
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)
X-TMN:	[AcdHTTRx52lu7kHWaeAQZbatTPLvRT/E]
Message-ID:	<BAY175-W315899B1CB94BF0A9EDB3CADD90@phx.gbl>
From:	Robert May <tpibob AT gmail DOT com>
To:	"cygwin AT cygwin DOT com" <cygwin AT cygwin DOT com>
Subject:	Re error after installing cygwin64 4.3.1.1
Date:	Wed, 27 Jan 2016 14:24:21 +1000
MIME-Version:	1.0
X-MIME-Autoconverted:	from quoted-printable to 8bit by delorie.com id u0R4Oed0012334

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
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname and ISOGG YTree 		 	   		  
--
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 -