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Subject:	Re: bcftools error running Make after installing update 2.4.1.1 to Cygwin64
To:	cygwin AT cygwin DOT com
References:	<BAY175-W34875F1AEC9896102CA3A3ADD90 AT phx DOT gbl>
From:	Marco Atzeri <marco DOT atzeri AT gmail DOT com>
Message-ID:	<56A88876.1040808@gmail.com>
Date:	Wed, 27 Jan 2016 10:05:58 +0100
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On 27/01/2016 05:53, Robert May wrote:
> I have had another look at Makefile and I changed c to gnu in this line 40 -std=gnu99
> CFLAGS   = -g -Wall -Wc++-compat -O2  -std=gnu99
>
> I had also removed -rdynamic in  line 185 so it now reads
> $(CC)  $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
>
> and ran make again
>
> Like sametools it has many warning essages about ‘expl’, ‘alloca’, ‘fileno’, ‘char’, this last one being the most prominent and ends with
>
> prob1.o: In function `mc_cal_y':
> /usr/local/bin/bcftools-1.3/prob1.c:320: undefined reference to `expl'
> /usr/local/bin/bcftools-1.3/prob1.c:320:(.text+0x1842): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `expl'
> collect2: error: ld returned 1 exit status
> Makefile:185: recipe for target 'bcftools' failed
> make: *** [bcftools] Error 1
>
> this is the same error message as in samtools collect2: error: ld returned 1 exit status
> but a different culprit prob1.o: In function `mc_cal_y':
>
>
>   Bob May

Bob,
it seems you are missing some includes

fileno is defined in
   /usr/include/stdio.h

alloca in
   /usr/include/alloca.h

expl is not available so use exp are workaround


That char is not defined seems VERY VERY strange

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