[Bioperl-l] Bioperl-live has (near) empty Bio::Root::Root?

[John Chen]

Hi Chris, Leon, Warren and Tristan,

Got it. Thank you so much. 

best,
John

On Saturday, April 13, 2013 1:37:36 PM UTC-4, John Chen wrote:
>
> Hi, 
>
> I have perlbrew with perl-5.8.9 installed. And I tried to get the 
> bioperl-live via Git following the instruction on bioperl official site: 
> http://www.bioperl.org/wiki/Using_Git 
>
> However, it seems the testing bioperl version encountered error (below) 
> immediately. 
> Manually checking the cloned bioperl-live revealed there is only one 
> module 
> HTTPget.pm under Bio/Root (see below), 
> I also check the online Github bioperl-live repository, the  Bio/Root 
> folder indeed only contain only one modeul:  HTTPget.pm 
>
> is this normal or I need to use some alternative approach to get the 
> bioperl (the CPAN package is rather old though)? 
>
> Thanks 
>
> John 
>
> *% perl -MBio::Perl -le 'print Bio::Perl->VERSION;'* 
> ------------------------------------------------------------------------------------------------------------ 
>
> Base class package *"Bio::Root::Root" is empty.* 
>     (Perhaps you need to 'use' the module which defines that package 
> first, 
>     or make that module available in @INC (@INC contains: 
> $HOME/src/bioperl-live/ 
> $HOME/perlbrew//perls/perl-5.8.9/lib/5.8.9/x86_64-linux 
> $HOME/perlbrew//perls/perl-5.8.9/lib/5.8.9 
> $HOME/perlbrew//perls/perl-5.8.9/lib/site_perl/5.8.9/x86_64-linux 
> $HOME/perlbrew//perls/perl-5.8.9/lib/site_perl/5.8.9 .). 
>  at $HOME/src/bioperl-live//Bio/Location/WidestCoordPolicy.pm line 80 
> BEGIN failed--compilation aborted at 
> $HOME/src/bioperl-live//Bio/Location/WidestCoordPolicy.pm line 80. 
> Compilation failed in require at 
> $HOME/src/bioperl-live//Bio/Location/Atomic.pm line 79. 
> BEGIN failed--compilation aborted at 
> $HOME/src/bioperl-live//Bio/Location/Atomic.pm line 79. 
> Compilation failed in require at (eval 1) line 3. 
>         ...propagated at $HOME/perlbrew//perls/perl-5.8.9/lib/5.8.9/
> base.pm 
> line 93. 
> BEGIN failed--compilation aborted at 
> $HOME/src/bioperl-live//Bio/Location/Simple.pm line 87. 
> Compilation failed in require at 
> $HOME/src/bioperl-live//Bio/Factory/FTLocationFactory.pm line 97. 
> BEGIN failed--compilation aborted at 
> $HOME/src/bioperl-live//Bio/Factory/FTLocationFactory.pm line 97. 
> Compilation failed in require at $HOME/src/bioperl-live//Bio/SeqIO.pm line 
> 328. 
> BEGIN failed--compilation aborted at $HOME/src/bioperl-live//Bio/SeqIO.pm 
> line 328. 
> Compilation failed in require at $HOME/src/bioperl-live//Bio/Perl.pm line 
> 120. 
> BEGIN failed--compilation aborted at $HOME/src/bioperl-live//Bio/Perl.pm 
> line 120. 
> Compilation failed in require. 
> BEGIN failed--compilation aborted. 
> ------------------------------------------------------------------------------------------------------------ 
>
> %ls $HOME/src/bioperl-live/Bio/Root/ 
> HTTPget.pm 
> ------------------------------------------------------------------------------------------------------------ 
>
>
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