[Bioperl-l] Installing Bioperl 1.6.1 on Mac OS 10.6.7

[Chris Fields]

Trina,

You shouldn't need AcePerl nor Graphviz.  BTW, Lincoln has, for all intents and purposes, deprecated AcePerl now, so we have removed it as a requirement.

Also, the latest version of BioPerl on CPAN is 1.6.901; I think some of these issues have been specifically addressed in that release.  Can you try that release?

chris

On Jun 6, 2011, at 4:37 PM, Trina McMahon wrote:

> Hi everyone,
> 
> I was having some trouble with Bio::SeqUtils->cat() earlier today and with Roy's help I debugged my code. But it was still not working properly. I sent my script to a friend and he successfully ran it on his machine, producing the desired output. I am now suspecting that I need to upgrade my perl and bioperl.  I hadn't upgraded anything in about 6 months (I was running ActivePerl-5.10 and BioPerl 1.6.0)..  So I ran my MacPorts upgrade, installed Perl 5.12, installed GraphViz, and configured CPAN as directed here:
> 
> http://www.sysarchitects.com/bioperl
> 
> but when I went to build bioperl 1.6.1, I got a lot of what look like fatal errors.  Also, none of my scripts using bioperl work using this new build.
> 
> Inspecting the errors, it seems like it is having trouble with AcePerl and maybe GraphViz (though this seemed to do ok with MacPorts??).  
> 
> Any advice welcome!  I saw in the archive that I might not be the only one with this problem, so I hope someone has a work-around??
> 
> thanks,
> trina
> 
> p.s. note that I am not using the perl that is installed with MacOS, I did a fresh installation in /opt/local/bin/ using MacPorts.  I also am pretty sure my path is not the problem (I changed it to reflect the new Perl location)
> 
> errors look like this:
> 
> /opt/local/bin/perl "-Iblib/arch" "-Iblib/lib" util/install.PLS util/install.pl
> Extracting install.pl (with variable substitutions)
>  LDS/AcePerl-1.92.tar.gz
>  /Developer/usr/bin/make -- OK
> Running make test
> PERL_DL_NONLAZY=1 /opt/local/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/basic.t ..... Waiting for remote acedb regression database to start up.  This may take a few minutes.
> t/basic.t ..... 2/10 Couldn't establish connection to database.  Aborting tests.
> t/basic.t ..... Dubious, test returned 60 (wstat 15360, 0x3c00)
> Failed 9/10 subtests 
> t/object.t .... 2/36 Couldn't establish connection to database.  Aborting tests.
> t/object.t .... Dubious, test returned 60 (wstat 15360, 0x3c00)
> Failed 35/36 subtests 
> t/sequence.t .. 2/54 Couldn't establish connection to database.  Aborting tests.
> t/sequence.t .. Dubious, test returned 60 (wstat 15360, 0x3c00)
> Failed 53/54 subtests 
> t/update.t .... 2/17 Couldn't establish connection to database.  Aborting tests.
> t/update.t .... Dubious, test returned 60 (wstat 15360, 0x3c00)
> Failed 16/17 subtests 
> 
> <...snip...>
> 
> Result: PASS
>  CJFIELDS/BioPerl-1.6.1.tar.gz
> Tests succeeded but one dependency not OK (Ace)
>  CJFIELDS/BioPerl-1.6.1.tar.gz
>  [dependencies] -- NA
> Running Build install
>  make test had returned bad status, won't install without force
> Failed during this command:
> LDS/AcePerl-1.92.tar.gz                      : make_test NO
> CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test NO one dependency not OK (Ace)
> 
> 
> -------------------------------------------------------------------------------------
> Katherine (Trina) McMahon, Associate Professor
> Goddess of Funkosity
> Departments of Civil and Environmental Engineering and Bacteriology
> Environmental Chemistry and Technology Program
> Limnology and Marine Science Program
> Microbiology Doctoral Training Program
> 
> **On sabbatical leave starting August 20, 2010**
> 
> Mailing Address:
> 3204 Engineering Hall, 1415 Engineering Drive
> University of Wisconsin - Madison, Madison, WI  53706-1691
> 
> Alternate Office:  5552 Microbial Sciences Building
> 
> Phone: 608/890-2836     Fax: 608/262-9865    
> Email: tmcmahon at engr.wisc.edu
> McMahon Lab: http://www.engr.wisc.edu/cee/faculty/mcmahon_katherine.html
> North Temperate Lakes Microbial Observatory: http://microbes.limnology.wisc.edu/
> 
> -------------------------------------------------------------------------------------
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