On 27/01/2016 05:53, Robert May wrote:
I have had another look at Makefile and I changed c to gnu in this line 40 -std=gnu99 CFLAGS = -g -Wall -Wc++-compat -O2 -std=gnu99 I had also removed -rdynamic in line 185 so it now reads $(CC) $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS) and ran make again Like sametools it has many warning essages about ‘expl’, ‘alloca’, ‘fileno’, ‘char’, this last one being the most prominent and ends with prob1.o: In function `mc_cal_y': /usr/local/bin/bcftools-1.3/prob1.c:320: undefined reference to `expl' /usr/local/bin/bcftools-1.3/prob1.c:320:(.text+0x1842): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `expl' collect2: error: ld returned 1 exit status Makefile:185: recipe for target 'bcftools' failed make: *** [bcftools] Error 1 this is the same error message as in samtools collect2: error: ld returned 1 exit status but a different culprit prob1.o: In function `mc_cal_y': Bob May
Bob, it seems you are missing some includes fileno is defined in /usr/include/stdio.h alloca in /usr/include/alloca.h expl is not available so use exp are workaround That char is not defined seems VERY VERY strange -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
