I am trying to compile a simulation program called COSI: http://www.broadinstitute.org/~sfs/cosi/cosi_1.2.1.tar
After unzipping it with tar xfp cosi_package.tar, I try to run make as stated in the README within the newly created directory cosi_1.2. Unfortunately, I get a lot of errors such as
coalescent.a(historical.o): In function `historical_process_pop_event':
historical.c:(.text+0x5c7): undefined reference to `log'
coalescent.a(historical.o): In function `historical_next_exp':
historical.c:(.text+0x76a): undefined reference to `exp'
../cosi_rand/random.a(ranbinom.o):ranbinom.c:(.text+0x702): more undefined references to `log' follow
collect2: ld returned 1 exit status
make[1]: *** [coalescent] Error 1
make[1]: Leaving directory `/home/myname/Desktop/cosi_1.2/cosi'
make: *** [all] Error 2
The MAKEFILE in the problematic sub-directory looks like this:
PACKAGE := coalescent
BINFILES := coalescent.c
SKIPFILES :=
ARFILE := $(PACKAGE).a
BINS := $(BINFILES:.c=)
PREFILES := $(wildcard *.c)
CFILES := $(filter-out $(SKIPFILES),$(PREFILES))
LIBFILES := $(filter-out $(BINFILES),$(CFILES))
OFILES := $(LIBFILES:.c=.o)
DFILES := $(CFILES:.c=.d)
FOO := $(ARFILE)(
BAR := )
AFILES := $(addprefix $(FOO), $(OFILES))
AFILES := $(addsuffix $(BAR), $(AFILES))
CC := gcc
CFLAGS := $(DEBUG) -O3 -Wall -ansi
all : $(BINS)
# rm *.d; rm *.o
install : $(BINS)
rm *.d; rm *.o
.PHONY : cleaninstall
cleaninstall :
rm $(BINS)
$(ARFILE) : $(AFILES)
$(AR) cr $(ARFILE) $(?:.c=.o)
$(RM) $(?:.c=.o)
$(BINS) : % : %.o $(ARFILE)
ranlib $(ARFILE)
$(CC) $(CFLAGS) -lm -v -o $@ [email protected] $(ARFILE) ../cosi_rand/random.a
%.d: %.c
@$(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $< \
| sed '\''s/\($*\)\.o[ :]*/coalescent.a(\1.o) $@ : /g'\'' > $@; \
[ -s $@ ] || rm -f $@'
-include $(DFILES)
Obviously, all the errors are missing mathematical functions. Hence I tried adding -lm to CFLAGS but it didn't help. Any suggestions what I could do?
-lm is a linker flag. It should appear at the end of the linker command:
$(CC) -v -o $@ [email protected] $(ARFILE) ../cosi_rand/random.a -lm
Apparently some compilers permit -l to appear anywhere. I still haven't found out which ones do, but my GCC wants them at the end, and in reverse order of dependency: if random.a needs libm, then libm should be linked in after random.a.
I also removed $(CFLAGS) from the linker command because you should pass linker options, not compiler options, when linking.
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