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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-W14DF8CC504AF6F9213BF6CADC70 AT phx DOT gbl>
From:	David Stacey <drstacey AT tiscali DOT co DOT uk>
Message-ID:	<56A693F5.7070000@tiscali.co.uk>
Date:	Mon, 25 Jan 2016 21:30:29 +0000
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On 25/01/16 21:00, Robert May wrote:
> many warnings are given in the following text - see end for error message
>
> echo '#define BCFTOOLS_VERSION "1.3"'> version.h
> gcc -g -Wall -Wc++-compat -O2  -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\"  -c -o main.o main.c
> gcc -g -Wall -Wc++-compat -O2  -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\"  -c -o vcfindex.o vcfindex.c
> vcfindex.c: In function ‘main_vcfindex’:
> vcfindex.c:209:9: warning: implicit declaration of function ‘alloca’ [-Wimplicit-function-declaration]
>           char*idx_fname = (char*)alloca(strlen(fname) + 5);
>           ^
> vcfindex.c:209:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
>           char*idx_fname = (char*)alloca(strlen(fname) + 5);

These warnings can be generated for a number of reasons. One is that the 
source code you are attempting to compile pre-dates this version of gcc. 
Another reason is that you are somehow using a combination of compiler 
switches that were never expected. A third reason is that the source 
code simply isn't well written, but the majority of Open Source 
contributors take great pride in their work.

In your case, it could be the compiler switches - see below.

> gcc -g -Wall -Wc++-compat -O2  -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\"  -c -o vcfcnv.o vcfcnv.c
> vcfcnv.c: In function ‘norm_prob’:
> vcfcnv.c:602:93: error: ‘M_PI’ undeclared (first use in this function)
>       return exp(-(baf-param->mean)*(baf-param->mean)*0.5/param->dev2) / param->norm / sqrt(2*M_PI*param->dev2);
>                                                                                               ^
> vcfcnv.c:602:93: note: each undeclared identifier is reported only once for each function it appears in
> vcfcnv.c: In function ‘main_vcfcnv’:
> vcfcnv.c:1349:9: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
>           if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";
>           ^
> vcfcnv.c: In function ‘norm_prob’:
> vcfcnv.c:603:1: warning: control reaches end of non-void function [-Wreturn-type]
>   }
>   ^

This looks like expected behaviour to me. Specifying '-std=c99' defines 
a __STRICT_ANSI__ macro, which in turn means that mathematical constants 
like M_PI are not defined. Using '-std=gnu99' instead should work. You 
may also find that this more relaxed compiler setting doesn't generate 
so many warnings.

Dave.


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