Fwd: [MacPorts] #45163: Prokka fails to build (some macports were used for the dependencies)

[Lawrence Velázquez]

Begin forwarded message:

> From: MacPorts <noreply at macports.org>
> Subject: [MacPorts] #45163: Prokka fails to build (some macports were used for the dependencies)
> Date: September 26, 2014 at 5:26:43 AM EDT
> To: hobbsilla at gmail.com, macports-tickets at lists.macosforge.org
> Reply-To: macports-dev at lists.macosforge.org
> 
> #45163: Prokka fails to build (some macports were used for the dependencies)
> -------------------------+--------------------------------
> Reporter:  hobbsilla@…  |      Owner:  macports-tickets@…
>     Type:  defect       |     Status:  new
> Priority:  Normal       |  Milestone:
> Component:  ports        |    Version:  2.3.1
> Keywords:               |       Port:
> -------------------------+--------------------------------
> I attempted to build my prokka database and get this abort message. Could
> someone help me figure out based on the provide output from my terminal
> where I could find a more detailed log that I could attach to this ticket?
> I used CPAN to install Bioperl. I believe cpanminus is in the macports but
> I'm not sure if I managed to install CPAN from elsewhere. I have
> ncbi_tools macports installed plus the blast+ through the source code just
> to cover my bases. I install GNU Parallel through the Macports. All of the
> other dependencies I installed from source code (HMMER, Aragorn, Prodigal
> and Infernal). Any help would be greatly appreciated.
> 
> {{{
> $ prokka --setupdb
> Can't locate XML/Simple.pm in @INC (@INC contains:
> /opt/local/lib/perl5/site_perl/5.12.5/darwin-thread-multi-2level
> /opt/local/lib/perl5/site_perl/5.12.5
> /opt/local/lib/perl5/vendor_perl/5.12.5/darwin-thread-multi-2level
> /opt/local/lib/perl5/vendor_perl/5.12.5 /opt/local/lib/perl5/5.12.5
> /darwin-thread-multi-2level /opt/local/lib/perl5/5.12.5
> /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl/5.12.4
> /darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.12.4
> /opt/local/lib/perl5/vendor_perl .) at
> /Users/elixir/Documents/Programming_Folder/bioinfo/prokka-1.10/bin/prokka
> line 25.
> }}}

To my Perl neophyte's eyes, it looks like you need to install XML-Simple.

    % sudo port install p5.12-xml-simple

vq