[Biodevelopers] Re: [BiO BB] Seqio and fmtseq

[Joe Landman]

On Mon, 2004-02-23 at 07:36, Stefanie Lager wrote:
> Thank you,
> 
> I really don't know much about compilation of c programs, so I don't
> know what "-D__unix" means, and how it should be added?

Ok, edit the "Makefile" and make the CFLAGS line look like this:

	CFLAGS= -g -O2 -Wall -Wshadow -D__unix

Then from the command prompt

	rm -f *.o
	make

You will get lots of warnings, but it should work.

Joe

> 
> Stefanie
> 
> > Did you add a
> > 
> > 	-D__unix
> > 
> > to the compile line?
> > 
> > [landman at protein.scalableinformatics.com:~/seqio-1.2.2]
> > 120 >./fmtseq
> > 
> > Input:  *none*     (format: *auto*)
> > Output:  *stdout*     (format: *none*)
> > Deflts:  -verbose  -gapin=-  -gapout=-  -bigalign
> > Options:  -all
> > 
> > Warning:  An input file and output format must be specified.
> > 
> > Commands (-option - set option,  -no... - unset option, ? -help - list
> > options,
> > -r -run - execute,  -q -quit - exit program, other - set input
> > file)
> > Enter:
> > 
> > I can package up this directory and build an RPM out of it if there is
> > interest.
> > 
> > Joe
> > 
> > On Mon, 2004-02-23 at 04:47, Stefanie Lager wrote:
> >> Hi,
> >> 
> >> I have problems to compile the Seqio library and specifically the
> >> fmtseq sequence format conversion program, on Linux. It seems as if
> >> line 150 in seqio.c and line 40 in fmtseq.c (extern char
> >> *sys_errlist[]) is in conflict with stdio.h (gcc version 3.2.2). I've
> >> tried to comment out these two lines, and then it compiles, but when
> >> I try to run fmtseq it crashes with "Segmentation fault". Does anyone
> >> know how to modify seqio.c and fmtseq.c, so they can be compiled on
> >> Linux?
> >> 
> >> Stefanie
> >> _________________________________________________________________
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> > --
> > Joe Landman <landman at scalableinformatics.com>
> > 
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