[BiO BB] Seqio and fmtseq

Stefanie Lager stefanielager at fastmail.ca
Mon Feb 23 08:25:42 EST 2004


I've tried adding -D__unix to the Makefile, but I still get the
"conflicting types for sys_errlist" for:

grepseq.c:21
seqio.c:150
fmtseq.c:40

No executables made, so I really don't see the difference?

Stefanie

> 
> 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
>>>> _________________________________________________________________
>>>> http://fastmail.ca/ - Fast Secure Web Email for Canadians
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>>> --
>>> Joe Landman <landman at scalableinformatics.com>
>>> 
>>> _______________________________________________
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>> _________________________________________________________________
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> 
> _______________________________________________
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