This is the mail archive of the
cygwin
mailing list for the Cygwin project.
FW: Re Samtools error after installing cygwin64 4.3.1.1
- From: Robert May <tpibob at gmail dot com>
- To: "cygwin at cygwin dot com" <cygwin at cygwin dot com>
- Date: Wed, 27 Jan 2016 21:23:43 +1000
- Subject: FW: Re Samtools error after installing cygwin64 4.3.1.1
- Authentication-results: sourceware.org; auth=none
- References: <BAY175-W315899B1CB94BF0A9EDB3CADD90 at phx dot gbl>,<BAY175-W36A8E62DEDB34EC2764606ADD90 at phx dot gbl>
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: tpibob@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
--
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