[Bioperl-l] bioperl errors
longbow leo
longbow0 at gmail.com
Mon Mar 25 08:42:38 UTC 2013
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
> >
> >
> >
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