[Bioperl-l] need help in Bio-SCF

neeti somaiya neetisomaiya at gmail.com
Wed Feb 21 03:19:14 EST 2007


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.

[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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