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Re: Re error after installing cygwin64 4.3.1.1
- From: Marco Atzeri <marco dot atzeri at gmail dot com>
- To: cygwin at cygwin dot com
- Date: Wed, 27 Jan 2016 09:52:07 +0100
- Subject: Re: Re error after installing cygwin64 4.3.1.1
- Authentication-results: sourceware.org; auth=none
- References: <BAY175-W315899B1CB94BF0A9EDB3CADD90 at phx dot gbl>
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@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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