[Bioperl-l] bioperl errors

[Fields, Christopher J]

On Mar 25, 2013, at 6:19 AM, Leon Timmermans <l.m.timmermans at students.uu.nl> wrote:

> On Thu, Mar 21, 2013 at 10:08 PM, liz wright <lzwright at gmail.com> wrote:
>> Hi, I just force installed bioperl on ubuntu linux as this approach was
>> proposed as a viable alternative when certain tests fail, but I would like
>> to check that the fail errors listed below will not significantly impair
>> bioperl usage as I am new to all this and don't really know how to
>> interpret the error messages.  Thanks, Liz Wright
>> 
>> 
>> * WARNING: Configuration was initially created with Module::Build
>>  version '0.38' but we are now using version '0.4003'.
>>  If errors occur, you must re-run the Build.PL or Makefile.PL script.
>> Will try to install symlinks to /usr/local/bin
>>  CJFIELDS/BioPerl-1.6.1.tar.gz
>>  sudo ./Build install  -- OK
>> Failed during this command:
>> LDS/AcePerl-1.92.tar.gz                      : make_test FAILED but
>> failure ignored because 'force' in effect
>> KMACLEOD/libxml-perl-0.08.tar.gz             : make_test FAILED but
>> failure ignored because 'force' in effect
>> TJMATHER/XML-DOM-1.44.tar.gz                 : make_test FAILED but
>> failure ignored because 'force' in effect
>> MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test FAILED but
>> failure ignored because 'force' in effect
>> BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test FAILED but
>> failure ignored because 'force' in effect
>> TODDR/XML-Parser-2.41.tar.gz                 : make NO
>> MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test FAILED but
>> failure ignored because 'force' in effect
>> MIROD/XML-Twig-3.42.tar.gz                   : make_test FAILED but
>> failure ignored because 'force' in effect
>> CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test FAILED but
>> failure ignored because 'force' in effect
> 
> Most of those are XML modules that need an external XML library. Force
> installing won't solve that problem. Installing expat (on my ubuntu
> that'd be libexpat1) should be the solution. Odds are the other
> failures are dependent failures that will also disappear.
> 
> Leon

Also, the version on CPAN has been updated to handle 'optional' dependencies; AcePerl for instance is pretty much in maintenance mode (maybe deprecated) and hasn't been updated in years.

chris