[Bioperl-l] Getting started

[Sean Davis]

I am just getting started with BioPerl on MacOS 10.3, Bioperl-1.4.  This is
one of the example scripts from the tutorial.  It results in the exception
given below.  My perl and OS information is listed below that.  What did I
forget to do?

Thanks,
Sean


  use Bio::Biblio;
  my $biblio = new Bio::Biblio (-access => 'biofetch');
  my $ref = $biblio->get_by_id('20063307');

  my $ids = ['20063307', '98276153'];
  my $refio = $biblio->get_all($ids);
  while ($ref = $refio->next_bibref) {
    print $ref->identifier, "\n";
  }



------------- EXCEPTION  -------------
MSG: retrieval type pipeline unsupported

STACK Bio::DB::Biblio::biofetch::get_seq_stream
/Library/Perl/5.8.1/Bio/DB/Biblio/biofetch.pm:237
STACK Bio::DB::DBFetch::get_Stream_by_id
/Library/Perl/5.8.1/Bio/DB/DBFetch.pm:194
STACK Bio::DB::Biblio::biofetch::get_by_id
/Library/Perl/5.8.1/Bio/DB/Biblio/biofetch.pm:153
STACK toplevel -:3

--------------------------------------

perl -V
Summary of my perl5 (revision 5.0 version 8 subversion 1 RC3) configuration:
  Platform:
    osname=darwin, osvers=7.0, archname=darwin-thread-multi-2level
    uname='darwin hampsten 7.0 darwin kernel version 6.0: fri jul 25
16:58:41 pdt 2003; root:xnu-344.frankd.rootsxnu-344.frankd~objrelease_ppc
power macintosh powerpc '
    config_args='-ds -e -Dprefix=/usr -Dccflags=-g  -pipe
-Dldflags=-Dman3ext=3pm -Duseithreads -Duseshrplib'
    hint=recommended, useposix=true, d_sigaction=define
    usethreads=define use5005threads=undef useithreads=define
usemultiplicity=define
    useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
    use64bitint=undef use64bitall=undef uselongdouble=undef
    usemymalloc=n, bincompat5005=undef
  Compiler:
    cc='cc', ccflags ='-g -pipe -pipe -fno-common -DPERL_DARWIN
-no-cpp-precomp -fno-strict-aliasing -I/usr/local/include',
    optimize='-Os',
    cppflags='-no-cpp-precomp -g -pipe -pipe -fno-common -DPERL_DARWIN
-no-cpp-precomp -fno-strict-aliasing -I/usr/local/include'
    ccversion='', gccversion='3.3 20030304 (Apple Computer, Inc. build
1495)', gccosandvers=''
    intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=4321
    d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=8
    ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t',
lseeksize=8
    alignbytes=8, prototype=define
  Linker and Libraries:
    ld='MACOSX_DEPLOYMENT_TARGET=10.3 cc', ldflags ='-L/usr/local/lib'
    libpth=/usr/local/lib /usr/lib
    libs=-ldbm -ldl -lm -lc
    perllibs=-ldl -lm -lc
    libc=/usr/lib/libc.dylib, so=dylib, useshrplib=true,
libperl=libperl.dylib
    gnulibc_version=''
  Dynamic Linking:
    dlsrc=dl_dyld.xs, dlext=bundle, d_dlsymun=undef, ccdlflags=' '
    cccdlflags=' ', lddlflags='-bundle -undefined dynamic_lookup
-L/usr/local/lib'


Characteristics of this binary (from libperl):
  Compile-time options: MULTIPLICITY USE_ITHREADS USE_LARGE_FILES
PERL_IMPLICIT_CONTEXT
  Locally applied patches:
        RC3
  Built under darwin
  Compiled at Sep 12 2003 19:50:49
  %ENV:
    PERL5LIB="/sw/lib/perl5:/sw/lib/perl5/darwin"
  @INC:
    /sw/lib/perl5/5.8.1/darwin-thread-multi-2level
    /sw/lib/perl5/5.8.1
    /sw/lib/perl5
    /sw/lib/perl5/darwin
    /System/Library/Perl/5.8.1/darwin-thread-multi-2level
    /System/Library/Perl/5.8.1
    /Library/Perl/5.8.1/darwin-thread-multi-2level
    /Library/Perl/5.8.1
    /Library/Perl
    /Network/Library/Perl/5.8.1/darwin-thread-multi-2level
    /Network/Library/Perl/5.8.1
    /Network/Library/Perl
    .
[holmes:~/Work/scratch] sdavis% perl -d temp.pl