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

[Trina McMahon]

duh!  Thanks, Chris.  That fixed it!!    And now I know how to check which version is most recent on CPAN.  :-)

trina

On Jun 6, 2011, at 11:46 PM, Chris Fields wrote:

> 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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>> 
>> 
>> _______________________________________________
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> 

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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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