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Re: bcftools error running Make after installing update to Cygwin64

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.


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