[Bioperl-l] Fwd: bioperl errors

[Leon Timmermans]

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