After a long time, I downloaded a program I co-developed and tried to recompile it on my Ubuntu Linux 12.04, but it seems it does not find math.h anymore. This may be because something has changed recently in gcc, but I can't figure out if it's something wrong in src/Makefile.am or a missing dependency:

Download from http://www.ub.edu/softevol/variscan/:

tar xzf variscan-2.0.2.tar.gz 
cd variscan-2.0.2/
make distclean
sh ./autogen.sh
make

I get: [...]

gcc -DNDEBUG -O3 -W -Wall -ansi -pedantic  -lm  -o variscan variscan.o statistics.o common.o linefile.o memalloc.o dlist.o errabort.o dystring.o intExp.o kxTok.o pop.o window.o free.o output.o readphylip.o readaxt.o readmga.o readmaf.o readhapmap.o readxmfa.o readmav.o ran1.o swcolumn.o swnet.o swpoly.o swref.o  
statistics.o: In function `calculate_Fu_and_Li_D':
statistics.c:(.text+0x497): undefined reference to `sqrt'
statistics.o: In function `calculate_Fu_and_Li_F':
statistics.c:(.text+0x569): undefined reference to `sqrt'
statistics.o: In function `calculate_Fu_and_Li_D_star':
statistics.c:(.text+0x63b): undefined reference to `sqrt'
statistics.o: In function `calculate_Fu_and_Li_F_star':
statistics.c:(.text+0x75c): undefined reference to `sqrt'
statistics.o: In function `calculate_Tajima_D':
statistics.c:(.text+0x85d): undefined reference to `sqrt'
statistics.o:statistics.c:(.text+0xcb1): more undefined references to `sqrt' follow
statistics.o: In function `calcRunMode21Stats':
statistics.c:(.text+0xe02): undefined reference to `log'
statistics.o: In function `correctedDivergence':
statistics.c:(.text+0xe5a): undefined reference to `log'
statistics.o: In function `calcRunMode22Stats':
statistics.c:(.text+0x104a): undefined reference to `sqrt'
statistics.o: In function `calculate_Fu_fs':
statistics.c:(.text+0x11a8): undefined reference to `fabsl'
statistics.c:(.text+0x11ca): undefined reference to `powl'
statistics.c:(.text+0x11f2): undefined reference to `logl'
statistics.o: In function `calculateStatistics':
statistics.c:(.text+0x13f2): undefined reference to `log'
collect2: ld returned 1 exit status
make[1]: *** [variscan] Error 1
make[1]: Leaving directory `/home/avilella/variscan/latest/variscan-2.0.2/src'
make: *** [all-recursive] Error 1

The libraries are there because this simple example works perfectly well:

$ gcc test.c -o test -lm
$ cat test.c 
#include <stdio.h>
#include <math.h>
int main(void)
{
        double x = 0.5;
        double result = sqrt(x);
        printf("The hyperbolic cosine of %lf is %lf\n", x, result);
        return 0;
}

Any ideas?