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

[Trina McMahon]

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)


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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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