[Bioperl-l] need help in Bio-SCF

Sean Davis sdavis2 at mail.nih.gov
Wed Feb 21 06:17:50 EST 2007


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


More information about the Bioperl-l mailing list