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Subject: Re: Re error after installing cygwin64 4.3.1.1
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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
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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


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