[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
>>>> _________________________________________________________________
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>>> --
>>> Joe Landman <landman at scalableinformatics.com>
>>>
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>
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