[Bioperl-l] bioperl errors

[longbow leo]

Hi Liz,

There are already "bioperl' and "bioperl-run" packages for ubuntu. It is
not necessary to install bioperl from source code.

Haizhou

On Fri, Mar 22, 2013 at 8:44 PM, liz wright <lzwright at gmail.com> wrote:

> As a follow up to my previous message, this gives a bit more information as
> to why the make tests failed:
>
>   make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/AcePerl-1.92.tar.gz                      : make_test NO
>  RSAVAGE/GraphViz-2.14.tgz                    : writemakefile NO
> '/usr/bin/perl Build.PL --installdirs site' returned status 512
>  TODDR/XML-Parser-2.41.tar.gz                 : make NO
>  KMACLEOD/libxml-perl-0.08.tar.gz             : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  TJMATHER/XML-DOM-1.44.tar.gz                 : make_test NO 2 dependencies
> missing (XML::Parser::PerlSAX,XML::Parser); additionally test harness
> failed
>  MIROD/XML-DOM-XPath-0.14.tar.gz              : make_test NO one dependency
> not OK (XML::DOM); additionally test harness failed
>  BJOERN/XML-SAX-Expat-0.40.tar.gz             : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  GRANTM/XML-Simple-2.20.tar.gz                : make_test NO one dependency
> not OK (XML::SAX::Expat)
>  MKUTTER/SOAP-Lite-0.715.tar.gz               : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  MIROD/XML-Twig-3.42.tar.gz                   : make_test NO one dependency
> not OK (XML::Parser); additionally test harness failed
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test NO 8 dependencies
> missing
>
> (Ace,XML::Simple,SOAP::Lite,GraphViz,XML::Parser,XML::Twig,XML::Parser::PerlSAX,XML::DOM::XPath)
>
> On Thu, Mar 21, 2013 at 5:08 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
> >
> >
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>