[Bioperl-l] problems with install Bundle::Bioperl

[Brian Osborne]

David,

I suggest you do 'force install libxml-perl' and try the install for
Bundle::BioPerl again. It's hard to know whether that single error in the
tests is important, and you may not even use modules that use XML::Parser
anyway. You can address any problems with libxml-perl and Bioperl if and
when they arise later.

I've had to do these forced installs a few times, no problems with Bioperl
so far.

Brian O.


-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of david_aaron at softhome.net
Sent: Wednesday, January 29, 2003 11:05 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] problems with install Bundle::Bioperl

Hi:

I am trying to install Bundle::BioPerl under CPAN shell, and I found some
problems in XML::Parser::PerlSAX, when I try to install it separately I
obtained the following messages

cpan> install XML::Parser::PerlSAX
CPAN: Storable loaded ok
Going to read /opt/cpan/Metadata
 Database was generated on Wed, 29 Jan 2003 14:49:32 GMT
Running install for module XML::Parser::PerlSAX
Running make for K/KM/KMACLEOD/libxml-perl-0.07.tar.gz
CPAN: Digest::MD5 loaded ok
Checksum for
/opt/cpan/sources/authors/id/K/KM/KMACLEOD/libxml-perl-0.07.tar.gz ok
Scanning cache /opt/cpan/build for sizes
libxml-perl-0.07
libxml-perl-0.07/t
libxml-perl-0.07/t/canon_xml_writer.t
libxml-perl-0.07/t/stream.t
libxml-perl-0.07/t/xp_sax.t
libxml-perl-0.07/t/subs.t
libxml-perl-0.07/t/amsterdam.t
libxml-perl-0.07/t/schema.t
libxml-perl-0.07/lib
libxml-perl-0.07/lib/XML
libxml-perl-0.07/lib/XML/Handler
libxml-perl-0.07/lib/XML/Handler/Sample.pm
libxml-perl-0.07/lib/XML/Handler/XMLWriter.pm
libxml-perl-0.07/lib/XML/Handler/CanonXMLWriter.pm
libxml-perl-0.07/lib/XML/Handler/Subs.pm
libxml-perl-0.07/lib/XML/SAX2Perl.pm
libxml-perl-0.07/lib/XML/Perl2SAX.pm
libxml-perl-0.07/lib/XML/PatAct
libxml-perl-0.07/lib/XML/PatAct/MatchName.pm
libxml-perl-0.07/lib/XML/PatAct/Amsterdam.pm
libxml-perl-0.07/lib/XML/PatAct/PatternTempl.pm
libxml-perl-0.07/lib/XML/PatAct/ToObjects.pm
libxml-perl-0.07/lib/XML/PatAct/ActionTempl.pm
libxml-perl-0.07/lib/XML/Parser
libxml-perl-0.07/lib/XML/Parser/PerlSAX.pm
libxml-perl-0.07/lib/XML/ESISParser.pm
libxml-perl-0.07/lib/Data
libxml-perl-0.07/lib/Data/Grove
libxml-perl-0.07/lib/Data/Grove/Parent.pm
libxml-perl-0.07/lib/Data/Grove/Visitor.pm
libxml-perl-0.07/lib/Data/Grove.pm
libxml-perl-0.07/doc
libxml-perl-0.07/doc/index.html
libxml-perl-0.07/doc/mirror.sh
libxml-perl-0.07/doc/modules.xml
libxml-perl-0.07/doc/interface-style.pod
libxml-perl-0.07/doc/UsingPatActModules.pod
libxml-perl-0.07/doc/PerlSAX.pod
libxml-perl-0.07/doc/CreatingPatActModules.pod
libxml-perl-0.07/doc/UsingPerlSAX.pod
libxml-perl-0.07/examples
libxml-perl-0.07/examples/perlsax-test.pl
libxml-perl-0.07/examples/myhandler.xml
libxml-perl-0.07/examples/schema.xml
libxml-perl-0.07/examples/schema.pl
libxml-perl-0.07/examples/esis-test.pl
libxml-perl-0.07/examples/myhandler.pl
libxml-perl-0.07/examples/MyHandler.pm
libxml-perl-0.07/libxml-perl-0.07.spec
libxml-perl-0.07/MANIFEST
libxml-perl-0.07/Changes
libxml-perl-0.07/libxml-perl.spec
libxml-perl-0.07/Makefile.PL
libxml-perl-0.07/ChangeLog
libxml-perl-0.07/README

 CPAN.pm: Going to build K/KM/KMACLEOD/libxml-perl-0.07.tar.gz

Checking if your kit is complete...
Looks good
Writing Makefile for libxml-perl
cp lib/XML/Handler/Subs.pm blib/lib/XML/Handler/Subs.pm
cp lib/XML/Perl2SAX.pm blib/lib/XML/Perl2SAX.pm
cp lib/XML/PatAct/MatchName.pm blib/lib/XML/PatAct/MatchName.pm
cp lib/XML/SAX2Perl.pm blib/lib/XML/SAX2Perl.pm
cp lib/XML/Handler/Sample.pm blib/lib/XML/Handler/Sample.pm
cp lib/XML/PatAct/ActionTempl.pm blib/lib/XML/PatAct/ActionTempl.pm
cp lib/XML/PatAct/ToObjects.pm blib/lib/XML/PatAct/ToObjects.pm
cp lib/Data/Grove/Visitor.pm blib/lib/Data/Grove/Visitor.pm
cp lib/XML/Handler/CanonXMLWriter.pm blib/lib/XML/Handler/CanonXMLWriter.pm
cp lib/Data/Grove/Parent.pm blib/lib/Data/Grove/Parent.pm
cp lib/XML/ESISParser.pm blib/lib/XML/ESISParser.pm
cp lib/Data/Grove.pm blib/lib/Data/Grove.pm
cp lib/XML/Parser/PerlSAX.pm blib/lib/XML/Parser/PerlSAX.pm
cp lib/XML/PatAct/PatternTempl.pm blib/lib/XML/PatAct/PatternTempl.pm
cp lib/XML/Handler/XMLWriter.pm blib/lib/XML/Handler/XMLWriter.pm
cp lib/XML/PatAct/Amsterdam.pm blib/lib/XML/PatAct/Amsterdam.pm
Manifying blib/man3/XML::Perl2SAX.3pm
Manifying blib/man3/XML::Handler::Subs.3pm
Manifying blib/man3/XML::PatAct::MatchName.3pm
Manifying blib/man3/XML::SAX2Perl.3pm
Manifying blib/man3/XML::PatAct::ActionTempl.3pm
Manifying blib/man3/XML::Handler::Sample.3pm
Manifying blib/man3/XML::PatAct::ToObjects.3pm
Manifying blib/man3/Data::Grove::Parent.3pm
Manifying blib/man3/XML::Handler::CanonXMLWriter.3pm
Manifying blib/man3/Data::Grove::Visitor.3pm
Manifying blib/man3/XML::ESISParser.3pm
Manifying blib/man3/XML::Parser::PerlSAX.3pm
Manifying blib/man3/Data::Grove.3pm
Manifying blib/man3/XML::PatAct::PatternTempl.3pm
Manifying blib/man3/XML::PatAct::Amsterdam.3pm
Manifying blib/man3/XML::Handler::XMLWriter.3pm
 /usr/bin/make  -- OK
Running make test
PERL_DL_NONLAZY=1 /usr/bin/perl5.8.0 "-MExtUtils::Command::MM" "-e"
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/amsterdam...........ok
t/canon_xml_writer....ok
t/schema..............ok
t/stream..............FAILED test 11
       Failed 1/11 tests, 90.91% okay
t/subs................ok
t/xp_sax..............ok
Failed Test Stat Wstat Total Fail  Failed  List of Failed
 ---------------------------------------------------------------------------
-
 ---
t/stream.t                11    1   9.09%  11
Failed 1/6 test scripts, 83.33% okay. 1/45 subtests failed, 97.78% okay.
make: *** [test_dynamic] Error 29
 /usr/bin/make test -- NOT OK
Running make install
 make test had returned bad status, won't install without force

Any idea or suggestions about what can be happening, thanks in advance
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