bcftools error running Make after installing update 2.4.1.1 to Cygwin64
Robert May
tpibob@gmail.com
Wed Jan 27 08:29:00 GMT 2016
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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