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From: Robert May <tpibob AT gmail DOT com>
To: "cygwin AT cygwin DOT com" <cygwin AT cygwin DOT com>
Subject: bcftools error running Make after installing update 2.4.1.1 to Cygwin64
Date: Wed, 27 Jan 2016 14:53:08 +1000
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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
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname and ISOGG YTree 		 	   		  
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