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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