Opened 10 years ago

Closed 10 years ago

#45163 closed defect (invalid)

Prokka fails to build (some macports were used for the dependencies)

Reported by: hobbsilla Owned by: macports-tickets@…
Priority: Normal Milestone:
Component: ports Version: 2.3.1
Keywords: Cc:
Port:

Description

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.

Change History (1)

comment:1 Changed 10 years ago by larryv (Lawrence Velázquez)

Resolution: invalid
Status: newclosed

There doesn’t seem to be any MacPorts problem here, so I’m going to close this ticket. I’ll forward your query to the macports-users mailing list, and hopefully someone there can help you out.

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