[Bioperl-l] could not load phrap error

[Jason Stajich]

You only need to do this if you want to use SeqFeature::Collection
otherwise you can ignore the error (I assume you get this during make
test?  You don't say). Also, Bugs have been fixed in that module as well
since 1.1.1 (a developer's release only) so I don't know that I would
trust that version of it too much.


To use DB_File on your system:

You will need to insure that BerkeleyDB is installed on your system in
order to use DB_File.

See the readme for the module:
http://www.cpan.org/modules/by-module/DB_File/DB_File-1.806.readme
http://www.sleepycat.com

-jason

On Thu, 5 Dec 2002, [iso-8859-1] eicke felipe wrote:

> Hi,
>   I removed the old version of bioperl and installed
> bioperl 1.1.1, but there is an error as following:
>
> Can't locate loadable object for module DB_File in
> @INC (@INC contains:
> /usr/local/lib/perl5/5.8.0/sun4-solaris
> /usr/local/lib/perl5/5.8.0
> /usr/local/lib/perl5/site_perl/5.8.0/sun4-solaris
> /usr/local/lib/perl5/site_perl/5.8.0
> /usr/local/lib/perl5/site_perl .) at
> /usr/local/lib/perl5/site_perl/5.8.0/Bio/SeqFeature/Collection.pm
> line 121
> Compilation failed in require at
> /usr/local/lib/perl5/site_perl/5.8.0/Bio/SeqFeature/Collection.pm
> line 121.
> BEGIN failed--compilation aborted at
> /usr/local/lib/perl5/site_perl/5.8.0/Bio/SeqFeature/Collection.pm
> line 121.
> Compilation failed in require at
> /usr/local/lib/perl5/site_perl/5.8.0/Bio/Assembly/Contig.pm
> line 214.
> BEGIN failed--compilation aborted at
> /usr/local/lib/perl5/site_perl/5.8.0/Bio/Assembly/Contig.pm
> line 214.
> Compilation failed in require at
> /usr/local/lib/perl5/site_perl/5.8.0/Bio/Assembly/IO/phrap.pm
> line 148.
> BEGIN failed--compilation aborted at
> /usr/local/lib/perl5/site_perl/5.8.0/Bio/Assembly/IO/phrap.pm
> line 148.
>
> When I try to install the DB_File-1.806 occours:
>
> #perl Makefile.PL
> Parsing config.in...
> Looks Good.
> Note (probably harmless): No library found for -ldb
> Writing Makefile for DB_File
>
> # make
> cp DB_File.pm blib/lib/DB_File.pm
> AutoSplitting blib/lib/DB_File.pm
> (blib/lib/auto/DB_File)
> gcc -c  -I/usr/local/BerkeleyDB/include
> -fno-strict-aliasing -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -O   -DVERSION=\"1.806\"
> -DXS_VERSION=\"1.806\" -fPIC
> "-I/usr/local/lib/perl5/5.8.0/sun4-solaris/CORE"
> -D_NOT_CORE  -DmDB_Prefix_t=size_t
> -DmDB_Hash_t=u_int32_t  version.c
> version.c:30:16: db.h: No such file or directory
> make: *** [version.o] Error 1
>
> Could somebody help me?
> Thanks.
> Eicke.
>
>
>
>
>
>
>
>
>
>
>
>  --- Jason Stajich <jason@cgt.mc.duke.edu> escreveu: >
> Bio::Assembly::IO was introduced post 1.0.2 if you
> > try and mix versions it
> > won't work.  This is because _load_module is a
> > method introduced after
> > 1.0.2 so in order to use Bio::Assembly::IO you
> > should use bioperl 1.1.1
> > developer release or the current CVS live version of
> > the code.  If you
> > have both on your system you will need to make sure
> > your PERL5LIB or
> > in-script INC variable has the more recent bioperl
> > BEFORE
> > the 1.0.2 version.
> >
> > (Bio::Root::IO is the specific module which has
> > extended its API to
> > include the _load_module utillity which previous was
> > a copy+paste
> > function in all the XXIO factories)
> >
> > 1.2 release is forthcoming (Dec 31) will of course
> > superceede all of this
> > and should cause none of these problems .
> >
> > -jason
> >
> > On Wed, 4 Dec 2002, [iso-8859-1] eicke felipe wrote:
> >
> > > Hi Folks,
> > >   I installed the bioperl-1.0.2 to compile some
> > perl
> > > codes but when I tried to compile the following
> > error
> > > appear:
> > >
> > > Bio::Assembly::IO: could not load phrap - for more
> > > details on supported formats please see the
> > > Assembly::IO docs
> > > Exception Can't locate object method
> > "_load_module"
> > > via package "Bio::Assembly::IO" at
> > >
> >
> /usr/local/lib/perl5/site_perl/5.8.0/Bio/Assembly/IO.pm
> > > line 167.
> > >
> > > Could anybody help me?
> > > Thanks, Eicke.
> > >
> > >
> > >
> >
> _______________________________________________________________________
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> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
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>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu