Re: bcftools error running Make after installing update 2.4.1.1 to Cygwin64

2016-01-27 Thread Marco Atzeri
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 -

bcftools error running Make after installing update 2.4.1.1 to Cygwin64

2016-01-26 Thread Robert May
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 agai

Re: bcftools error running Make after installing update 2.4.1.1 to Cygwin64

2016-01-25 Thread Duncan Roe
On Mon, Jan 25, 2016 at 09:30:29PM +, David Stacey wrote: > On 25/01/16 21:00, Robert May wrote: > >many warnings are given in the following text - see end for error message > > > >echo '#define BCFTOOLS_VERSION "1.3"'> version.h > >gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 > >-

Re: bcftools error running Make after installing update 2.4.1.1 to Cygwin64

2016-01-25 Thread David Stacey
On 25/01/16 21:00, Robert May wrote: many warnings are given in the following text - see end for error message echo '#define BCFTOOLS_VERSION "1.3"'> version.h gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o main.o main.c gcc -g -Wall

bcftools error running Make after installing update 2.4.1.1 to Cygwin64

2016-01-25 Thread Robert May
error running Make after installing update 2.4.1.1 to Cygwin64 Robert@DESKTOP-14EL82S /usr/local/bin/bcftools-1.3 $ make   many warnings are given in the following text - see end for error message echo '#define BCFTOOLS_VERSION "1.3"'> version.h gcc -g -Wall -Wc++-compat -O2  -std=c99 -I. -Ihtsl