MarcoYes got samtools configure make install
samtools
= samtools index appears
What I did
line 26 added -std=gnu99
line 31 added -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=logline 87 removed -rdynamic
am about to try the program out
Bob
Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname
and ISOGG YTree
> From: tpi...@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
>
> 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
> DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler
> Surname and ISOGG YTree
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