[BiO BB] Seqio and fmtseq

Stefanie Lager stefanielager at fastmail.ca
Mon Feb 23 07:36:32 EST 2004


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?

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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