[Bioperl-l] BioPerl installation on Solaris

[Thomas, Daryl]

Hello,

I am having a bit of trouble installing BioPerl on Solaris.  A few of the
test scripts (such as parsing a GenBank file) work properly, but I am not
able to use Bio::Tools::BPlite to parse BLAST output.  In fact, the script
can't even be interpreted.  Is there something special about installing
BioPerl on Solaris 2.8?  I have included my sample.pl file, the error
message I receive, and the perl version information below.

Daryl Thomas
Perlegen Sciences, Inc.


----------------------------------------------------------------------------
File: sample.pl
----------------------------------------------------------------------------
#!/usr/bin/perl -w

# use lib "/home1/dthoma/bioperl-0.7.0/Bio/Tools/";
use Bio::Tools::BPlite;

my $report = BPlite->new(-fh=>\*STDIN);
# my $report = new BPlite(-fh=>\*STDIN);

print "\n\nQuery: ",$report->query, "\tDatabase: ",$report->database,"\n";
while(my $sbjct = $report->nextSbjct) {
  print "\nSubject: ",$sbjct->name,"";
  while (my $hsp = $sbjct->nextHSP) {
    print "\n\tScore",          $hsp->score;
    print "\n\tBits",           $hsp->bits;
    print "\n\tPercent",        $hsp->percent;
    print "\n\tP",              $hsp->P;
    print "\n\tMatch\tMatch",   $hsp->match;
    print "\n\tPositive",       $hsp->positive;
    print "\n\tLength",         $hsp->length;
    print "\n\tQuerySeq",       $hsp->querySeq;
    print "\n\tSubjectSeq",     $hsp->sbjctSeq;
    print "\n\tHomologySeq",    $hsp->homologyseq;
    print "\nQuery\tStart",     $hsp->query->start;
    print "\nQuery\tEnd",       $hsp->query->end;
    print "\nQuery\tSeqname",   $hsp->query->seqname;
    print "\nSubject\tStart",   $hsp->sbjct->start;
    print "\nSubject\tEnd",     $hsp->sbjct->end;
    print "\nSubject\tSeqname", $hsp->sbjct->seqname;
    print "\nSubject\tOverlaps",$hsp->sbjct->overlaps($exon);
  }
}
----------------------------------------------------------------------------
error message:
----------------------------------------------------------------------------
Name "main::exon" used only once: possible typo at sample.pl line 29.
Can't locate object method "new" via package "BPlite" at sample.pl line 6.
----------------------------------------------------------------------------


Summary of my perl5 (5.0 patchlevel 5 subversion 3) configuration:
  Platform:
    osname=solaris, osvers=2.8, archname=sun4-solaris
    uname='sunos localhost 5.8 sun4u sparc sunw,ultra-1 '
    hint=previous, useposix=true, d_sigaction=define
    usethreads=undef useperlio=undef d_sfio=undef
  Compiler:
    cc='cc', optimize='-xO3 -xdepend', gccversion=
    cppflags=''
    ccflags =''
    stdchar='char', d_stdstdio=define, usevfork=false
    intsize=4, longsize=4, ptrsize=4, doublesize=8
    d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
    alignbytes=8, usemymalloc=n, prototype=define
  Linker and Libraries:
    ld='cc', ldflags =''
    libpth=/lib /usr/lib /usr/ccs/lib
    libs=-lsocket -lnsl -ldl -lm -lc -lcrypt
    libc=/lib/libc.so, so=so, useshrplib=true, libperl=libperl.so
  Dynamic Linking:
    dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-R
/usr/perl5/5.00503/sun4-solaris/CORE'
    cccdlflags='-KPIC', lddlflags='-G'


Characteristics of this binary (from libperl): 
  Built under solaris
  Compiled at Dec 22 1999 00:00:57
  @INC:
    /usr/perl5/5.00503/sun4-solaris
    /usr/perl5/5.00503
    /usr/perl5/site_perl/5.005/sun4-solaris
    /usr/perl5/site_perl/5.005
    .