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Re: bcftools error running Make after installing update to Cygwin64

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

it seems you are missing some includes

fileno is defined in

alloca in

expl is not available so use exp are workaround

That char is not defined seems VERY VERY strange

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