[Bioperl-l] need help in Bio-SCF

neeti somaiya neetisomaiya at gmail.com
Wed Feb 21 07:25:26 EST 2007


Thanks. It resolved my problem.

On 2/21/07, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
> On Wednesday 21 February 2007 03:19, neeti somaiya wrote:
> > Hi All,
> >
> > I downloaded module
> > Bio-SCF-1.01<http://search.cpan.org/%7Elds/Bio-SCF-1.01/>from CPAN.
> > And I am trying to install it when I got the following error. Can
> someone
> > please guide me.
>
> You will probably need to read the INSTALL document.  You need to install
> a
> couple of libraries first.  Looks like you don't have the staden io-lib
> installed.
>
>
> > [root at ps2288 Bio-SCF-1.01]# perl Makefile.PL
> > Checking if your kit is complete...
> > Looks good
> > Note (probably harmless): No library found for -lread
> > Writing Makefile for Bio::SCF
> >
> > [root at ps2288 Bio-SCF-1.01]# make
> > cp SCF.pm blib/lib/Bio/SCF.pm
> > cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm
> > /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp  -typemap
> > /usr/lib/perl5/5.8.5/ExtUtils/typemap  SCF.xs > SCF.xsc && mv SCF.xsc
> SCF.c
> > Please specify prototyping behavior for SCF.xs (see perlxs manual)
> > gcc -c   -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBUGGING
> > -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
> > -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -m32 -march=i386
> > -mtune=pentium4   -DVERSION=\"1.01\" -DXS_VERSION=\"1.01\" -fPIC
> > "-I/usr/lib/perl5/5.8.5/i386-linux-thread-multi/CORE"  -DLITTLE_ENDIAN
> > SCF.c SCF.xs:12:24: io_lib/scf.h: No such file or directory
> > SCF.xs:13:26: io_lib/mFILE.h: No such file or directory
> > SCF.xs: In function `XS_Bio__SCF_get_scf_pointer':
> > SCF.xs:27: error: `Scf' undeclared (first use in this function)
> > SCF.xs:27: error: (Each undeclared identifier is reported only once
> > SCF.xs:27: error: for each function it appears in.)
> > SCF.xs:27: error: `scf_data' undeclared (first use in this function)
> > SCF.xs: In function `XS_Bio__SCF_get_scf_fpointer':
> > SCF.xs:66: error: `Scf' undeclared (first use in this function)
> > SCF.xs:66: error: `scf_data' undeclared (first use in this function)
> > SCF.xs:68: error: `mFILE' undeclared (first use in this function)
> > SCF.xs:68: error: `mf' undeclared (first use in this function)
> > SCF.xs: In function `XS_Bio__SCF_scf_free':
> > SCF.xs:89: error: `Scf' undeclared (first use in this function)
> > SCF.xs:89: error: syntax error before ')' token
> > SCF.xs: In function `XS_Bio__SCF_get_comments':
> > SCF.xs:95: error: `Scf' undeclared (first use in this function)
> > SCF.xs:95: error: `scf_data' undeclared (first use in this function)
> > SCF.xs:95: error: syntax error before ')' token
> > SCF.xs: In function `XS_Bio__SCF_set_comments':
> > SCF.xs:108: error: `Scf' undeclared (first use in this function)
> > SCF.xs:108: error: `scf_data' undeclared (first use in this function)
> > SCF.xs:108: error: syntax error before ')' token
> > SCF.xs: In function `XS_Bio__SCF_scf_write':
> > SCF.xs:121: error: `Scf' undeclared (first use in this function)
> > SCF.xs:121: error: `scf_data' undeclared (first use in this function)
> > SCF.xs:121: error: syntax error before ')' token
> > SCF.xs: In function `XS_Bio__SCF_scf_fwrite':
> > SCF.xs:135: error: `mFILE' undeclared (first use in this function)
> > SCF.xs:135: error: `mf' undeclared (first use in this function)
> > SCF.xs:137: error: `Scf' undeclared (first use in this function)
> > SCF.xs:137: error: `scf_data' undeclared (first use in this function)
> > SCF.xs:137: error: syntax error before ')' token
> > SCF.xs: In function `XS_Bio__SCF_get_from_header':
> > SCF.xs:159: error: `Scf' undeclared (first use in this function)
> > SCF.xs:159: error: `scf_data' undeclared (first use in this function)
> > SCF.xs:159: error: syntax error before ')' token
> > SCF.xs: In function `XS_Bio__SCF_get_at':
> > SCF.xs:186: error: `Scf' undeclared (first use in this function)
> > SCF.xs:186: error: `scf_data' undeclared (first use in this function)
> > SCF.xs:186: error: syntax error before ')' token
> > SCF.xs: In function `XS_Bio__SCF_set_base_at':
> > SCF.xs:242: error: `Scf' undeclared (first use in this function)
> > SCF.xs:242: error: `scf_data' undeclared (first use in this function)
> > SCF.xs:242: error: syntax error before ')' token
> > SCF.xs: In function `XS_Bio__SCF_set_at':
> > SCF.xs:255: error: `Scf' undeclared (first use in this function)
> > SCF.xs:255: error: `scf_data' undeclared (first use in this function)
> > SCF.xs:255: error: syntax error before ')' token
> > make: *** [SCF.o] Error 1
>



-- 
-Neeti
Even my blood says, B positive


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