James
No joy
run together or individualy
$ ./configure CFLAGS=-STD=C99
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in `/usr/local/bin/samtools-1.3':
configure: error: C compiler cannot create executables
See `config.log' for more details
$ ./configure CFLAGS=C99
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in `/usr/local/bin/samtools-1.3':
configure: error: C compiler cannot create executables
See `config.log' for more details
$ ./configure CFLAGS=-std
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in `/usr/local/bin/samtools-1.3':
configure: error: C compiler cannot create executables
See `config.log' for more details
thanks
bob
Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname
and ISOGG YTree
> Date: Thu, 14 Jan 2016 13:56:55 +0000
> From: j...@sanger.ac.uk
> To: tpi...@gmail.com
> CC: samtools-help@lists.sourceforge.net
> Subject: Re: [Samtools-help] Samtools makefile error
>
> On Thu, Jan 14, 2016 at 11:13:53PM +1000, Robert May wrote:
> > 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:139: recipe for target 'samtools' failed
> > make: *** [samtools] Error 1
>
> The linux man pages for expl and logl seeems to imply that
> ./configure CFLAGS=-std=c99 should be sufficient to get this working.
>
> I haven't tested it though, but either way the configure script will
> need these additional functions adding and some checks for how to
> enable them.
>
> James
>
> --
> James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
> | Plurima gyrabant gymbolitare vabo;
> A Staden Package developer: | Et Borogovorum mimzebant undique formae,
> https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
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