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Re: bcftools error running Make after installing update 2.4.1.1 to Cygwin64
- From: Marco Atzeri <marco dot atzeri at gmail dot com>
- To: cygwin at cygwin dot com
- Date: Wed, 27 Jan 2016 10:05:58 +0100
- Subject: Re: bcftools error running Make after installing update 2.4.1.1 to Cygwin64
- Authentication-results: sourceware.org; auth=none
- References: <BAY175-W34875F1AEC9896102CA3A3ADD90 at phx dot gbl>
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
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