[Bioperl-l] bioperl 1.6 installation on vista with perl 5.10

Johnathan Dalzell jdalzell03 at qub.ac.uk
Mon Aug 3 23:18:24 UTC 2009 

Hi, I've been trying to install Bioperl 1.6.0 onto strawberry perl 5.10 and the activePerl equivalent.  I'm wrking through vista, and ovver multiple times, this is the furthest I can get through installation....


Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] a
  - will install all scripts
Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n] y
  - will run internet-requiring tests
Encountered CODE ref, using dummy placeholder at C:/strawberry/perl/lib/Data/Dumper.pm lin
e 190, <STDIN> line 9.
Creating new 'Build' script for 'BioPerl' version '1.006000'
---- Unsatisfied dependencies detected during ----
----       CJFIELDS/BioPerl-1.6.0.tar.gz      ----
    SOAP::Lite [requires]
    GraphViz [requires]
    Convert::Binary::C [requires]
    Algorithm::Munkres [requires]
    XML::Twig [requires]
    DB_File [requires]
    Set::Scalar [requires]
    XML::Parser::PerlSAX [requires]
    XML::Writer [requires]
    XML::SAX::Writer [requires]
    Clone [requires]
    XML::DOM::XPath [requires]
    PostScript::TextBlock [requires]
Running Build test
  Delayed until after prerequisites
Running Build install
  Delayed until after prerequisites
Running install for module 'SOAP::Lite'
Running make for M/MK/MKUTTER/SOAP-Lite-0.710.08.tar.gz
Checksum for C:\strawberry\cpan\sources\authors\id\M\MK\MKUTTER\SOAP-Lite-0.710.08.tar.gz
ok
  CPAN.pm: Going to build M/MK/MKUTTER/SOAP-Lite-0.710.08.tar.gz
We are about to install SOAP::Lite and for your convenience will provide
you with list of modules and prerequisites, so you'll be able to choose
only modules you need for your configuration.
XMLRPC::Lite, UDDI::Lite, and XML::Parser::Lite are included by default.
Installed transports can be used for both SOAP::Lite and XMLRPC::Lite.
Press <enter> to see the detailed list.
Feature                       Prerequisites                Install?
----------------------------- ---------------------------- --------
Core Package                  [*] Scalar::Util             always
                              [*] Test::More
                              [*] URI
                              [*] MIME::Base64
                              [*] version
                              [*] XML::Parser (v2.23)
Client HTTP support           [*] LWP::UserAgent           always
Client HTTPS support          [ ] Crypt::SSLeay            [ no ]
Client SMTP/sendmail support  [ ] MIME::Lite               [ no ]
Client FTP support            [*] IO::File                 [ yes ]
                              [*] Net::FTP
Standalone HTTP server        [*] HTTP::Daemon             [ yes ]
Apache/mod_perl server        [ ] Apache                   [ no ]
FastCGI server                [ ] FCGI                     [ no ]
POP3 server                   [ ] MIME::Parser             [ no ]
                              [*] Net::POP3
IO server                     [*] IO::File                 [ yes ]
MQ transport support          [ ] MQSeries                 [ no ]
JABBER transport support      [ ] Net::Jabber              [ no ]
MIME messages                 [ ] MIME::Parser             [ no ]
DIME messages                 [*] IO::Scalar (v2.105)      [ no ]
                              [ ] DIME::Tools (v0.03)
                              [ ] Data::UUID (v0.11)
SSL Support for TCP Transport [ ] IO::Socket::SSL          [ no ]
Compression support for HTTP  [*] Compress::Zlib           [ yes ]
MIME interoperability w/ Axis [ ] MIME::Parser (v6.106)    [ no ]
--- An asterix '[*]' indicates if the module is currently installed.
Do you want to proceed with this configuration? [yes] yes
Checking if your kit is complete...
Looks good
Writing Makefile for SOAP::Lite
cp lib/SOAP/Client.pod blib\lib\SOAP\Client.pod
cp lib/UDDI/Lite.pm blib\lib\UDDI\Lite.pm
cp lib/SOAP/Packager.pm blib\lib\SOAP\Packager.pm
cp lib/XML/Parser/Lite.pm blib\lib\XML\Parser\Lite.pm
cp lib/SOAP/Transport/LOOPBACK.pm blib\lib\SOAP\Transport\LOOPBACK.pm
cp lib/XMLRPC/Transport/TCP.pm blib\lib\XMLRPC\Transport\TCP.pm
cp lib/SOAP/Transport/JABBER.pm blib\lib\SOAP\Transport\JABBER.pm
cp lib/OldDocs/SOAP/Transport/TCP.pm blib\lib\OldDocs\SOAP\Transport\TCP.pm
cp lib/SOAP/Transport/MAILTO.pm blib\lib\SOAP\Transport\MAILTO.pm
cp lib/OldDocs/SOAP/Transport/POP3.pm blib\lib\OldDocs\SOAP\Transport\POP3.pm
cp lib/Apache/SOAP.pm blib\lib\Apache\SOAP.pm
cp lib/SOAP/Schema.pod blib\lib\SOAP\Schema.pod
cp lib/SOAP/Test.pm blib\lib\SOAP\Test.pm
cp lib/Apache/XMLRPC/Lite.pm blib\lib\Apache\XMLRPC\Lite.pm
cp lib/XMLRPC/Transport/HTTP.pm blib\lib\XMLRPC\Transport\HTTP.pm
cp lib/SOAP/Transport/MQ.pm blib\lib\SOAP\Transport\MQ.pm
cp lib/SOAP/Transport/POP3.pm blib\lib\SOAP\Transport\POP3.pm
cp lib/SOAP/Deserializer.pod blib\lib\SOAP\Deserializer.pod
cp lib/SOAP/Data.pod blib\lib\SOAP\Data.pod
cp lib/SOAP/Server.pod blib\lib\SOAP\Server.pod
cp lib/SOAP/Transport/IO.pm blib\lib\SOAP\Transport\IO.pm
cp lib/SOAP/Lite/Utils.pm blib\lib\SOAP\Lite\Utils.pm
cp lib/SOAP/Header.pod blib\lib\SOAP\Header.pod
cp lib/SOAP/Constants.pm blib\lib\SOAP\Constants.pm
cp lib/SOAP/Lite/Packager.pm blib\lib\SOAP\Lite\Packager.pm
cp lib/SOAP/SOM.pod blib\lib\SOAP\SOM.pod
cp lib/XMLRPC/Transport/POP3.pm blib\lib\XMLRPC\Transport\POP3.pm
cp lib/SOAP/Lite/Deserializer/XMLSchema1999.pm blib\lib\SOAP\Lite\Deserializer\XMLSchema19
99.pm
cp lib/XMLRPC/Lite.pm blib\lib\XMLRPC\Lite.pm
cp lib/OldDocs/SOAP/Lite.pm blib\lib\OldDocs\SOAP\Lite.pm
cp lib/SOAP/Transport.pod blib\lib\SOAP\Transport.pod
cp lib/OldDocs/SOAP/Transport/HTTP.pm blib\lib\OldDocs\SOAP\Transport\HTTP.pm
cp lib/SOAP/Lite/Deserializer/XMLSchema2001.pm blib\lib\SOAP\Lite\Deserializer\XMLSchema20
01.pm
cp lib/SOAP/Trace.pod blib\lib\SOAP\Trace.pod
cp lib/IO/SessionData.pm blib\lib\IO\SessionData.pm
cp lib/XMLRPC/Test.pm blib\lib\XMLRPC\Test.pm
cp lib/OldDocs/SOAP/Transport/MQ.pm blib\lib\OldDocs\SOAP\Transport\MQ.pm
cp lib/OldDocs/SOAP/Transport/FTP.pm blib\lib\OldDocs\SOAP\Transport\FTP.pm
cp lib/OldDocs/SOAP/Transport/JABBER.pm blib\lib\OldDocs\SOAP\Transport\JABBER.pm
cp lib/SOAP/Transport/TCP.pm blib\lib\SOAP\Transport\TCP.pm
cp lib/SOAP/Utils.pod blib\lib\SOAP\Utils.pod
cp lib/IO/SessionSet.pm blib\lib\IO\SessionSet.pm
cp lib/SOAP/Transport/HTTP.pm blib\lib\SOAP\Transport\HTTP.pm
cp lib/SOAP/Lite/Deserializer/XMLSchemaSOAP1_2.pm blib\lib\SOAP\Lite\Deserializer\XMLSchem
aSOAP1_2.pm
cp lib/OldDocs/SOAP/Transport/IO.pm blib\lib\OldDocs\SOAP\Transport\IO.pm
cp lib/SOAP/Serializer.pod blib\lib\SOAP\Serializer.pod
cp lib/SOAP/Lite/Deserializer/XMLSchemaSOAP1_1.pm blib\lib\SOAP\Lite\Deserializer\XMLSchem
aSOAP1_1.pm
cp lib/OldDocs/SOAP/Transport/LOCAL.pm blib\lib\OldDocs\SOAP\Transport\LOCAL.pm
cp lib/SOAP/Transport/LOCAL.pm blib\lib\SOAP\Transport\LOCAL.pm
cp lib/SOAP/Fault.pod blib\lib\SOAP\Fault.pod
cp lib/SOAP/Lite.pm blib\lib\SOAP\Lite.pm
cp lib/OldDocs/SOAP/Transport/MAILTO.pm blib\lib\OldDocs\SOAP\Transport\MAILTO.pm
cp lib/SOAP/Transport/FTP.pm blib\lib\SOAP\Transport\FTP.pm
C:\strawberry\perl\bin\perl.exe -MExtUtils::Command -e "cp" -- bin/SOAPsh.pl blib\script\S
OAPsh.pl
pl2bat.bat blib\script\SOAPsh.pl
C:\strawberry\perl\bin\perl.exe -MExtUtils::Command -e "cp" -- bin/stubmaker.pl blib\scrip
t\stubmaker.pl
pl2bat.bat blib\script\stubmaker.pl
C:\strawberry\perl\bin\perl.exe -MExtUtils::Command -e "cp" -- bin/XMLRPCsh.pl blib\script
\XMLRPCsh.pl
pl2bat.bat blib\script\XMLRPCsh.pl
  MKUTTER/SOAP-Lite-0.710.08.tar.gz
  C:\strawberry\c\bin\dmake.EXE -- OK
Running make test
C:\strawberry\perl\bin\perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib\lib'
, 'blib\arch')" t/01-core.t t/010-serializer.t t/012-cloneable.t t/013-array-deserializati
on.t t/014_UNIVERSAL_use.t t/015_UNIVERSAL_can.t t/02-payload.t t/03-server.t t/04-attach.
t t/05-customxml.t t/06-modules.t t/07-xmlrpc_payload.t t/08-schema.t t/096_characters.t t
/097_kwalitee.t t/098_pod.t t/099_pod_coverage.t t/IO/SessionData.t t/IO/SessionSet.t t/SO
AP/Data.t t/SOAP/Serializer.t t/SOAP/Lite/Packager.t t/SOAP/Lite/Deserializer/XMLSchema199
9.t t/SOAP/Lite/Deserializer/XMLSchema2001.t t/SOAP/Lite/Deserializer/XMLSchemaSOAP1_1.t t
/SOAP/Lite/Deserializer/XMLSchemaSOAP1_2.t t/SOAP/Schema/WSDL.t t/SOAP/Transport/FTP.t t/S
OAP/Transport/HTTP.t t/SOAP/Transport/IO.t t/SOAP/Transport/LOCAL.t t/SOAP/Transport/MAILT
O.t t/SOAP/Transport/MQ.t t/SOAP/Transport/POP3.t t/SOAP/Transport/HTTP/CGI.t t/XML/Parser
/Lite.t t/XMLRPC/Lite.t
t/01-core.t .................................. ok
t/010-serializer.t ........................... ok
t/012-cloneable.t ............................ ok
t/013-array-deserialization.t ................ ok
t/014_UNIVERSAL_use.t ........................ ok
t/015_UNIVERSAL_can.t ........................ ok
t/02-payload.t ............................... ok
t/03-server.t ................................ ok
t/04-attach.t ................................ skipped: Could not find MIME::Parser - is M
IME::Tools installed? Aborting.
t/05-customxml.t ............................. ok
t/06-modules.t ............................... ok
t/07-xmlrpc_payload.t ........................ ok
t/08-schema.t ................................ ok
t/096_characters.t ........................... skipped: (no reason given)
t/097_kwalitee.t ............................. skipped: (no reason given)
t/098_pod.t .................................. skipped: (no reason given)
t/099_pod_coverage.t ......................... skipped: (no reason given)
t/IO/SessionData.t ........................... ok
t/IO/SessionSet.t ............................ ok
t/SOAP/Data.t ................................ ok
t/SOAP/Lite/Deserializer/XMLSchema1999.t ..... ok
t/SOAP/Lite/Deserializer/XMLSchema2001.t ..... ok
t/SOAP/Lite/Deserializer/XMLSchemaSOAP1_1.t .. ok
t/SOAP/Lite/Deserializer/XMLSchemaSOAP1_2.t .. ok
t/SOAP/Lite/Packager.t ....................... ok
t/SOAP/Schema/WSDL.t ......................... ok
t/SOAP/Serializer.t .......................... 1/12 Use of uninitialized value $values[0]
in join or string at C:\strawberry\cpan\build\SOAP-Lite-0.710.08-wfOzhM\blib\lib/SOAP/Lite
.pm line 1376.
Use of uninitialized value $values[0] in join or string at C:\strawberry\cpan\build\SOAP-L
ite-0.710.08-wfOzhM\blib\lib/SOAP/Lite.pm line 1376.
Use of uninitialized value $values[0] in join or string at C:\strawberry\cpan\build\SOAP-L
ite-0.710.08-wfOzhM\blib\lib/SOAP/Lite.pm line 1376.
Use of uninitialized value $values[0] in join or string at C:\strawberry\cpan\build\SOAP-L
ite-0.710.08-wfOzhM\blib\lib/SOAP/Lite.pm line 1376.
t/SOAP/Serializer.t .......................... ok
t/SOAP/Transport/FTP.t ....................... 1/7 Use of uninitialized value in split at
C:\strawberry\cpan\build\SOAP-Lite-0.710.08-wfOzhM\blib\lib/SOAP/Transport/FTP.pm line 55.
substr outside of string at C:\strawberry\cpan\build\SOAP-Lite-0.710.08-wfOzhM\blib\lib/SO
AP/Transport/FTP.pm line 56.
Use of uninitialized value $_[1] in join or string at C:/STRAWB~1/perl/lib/IO/Socket/INET.
pm line 117.
Use of uninitialized value $server in concatenation (.) or string at C:\strawberry\cpan\bu
ild\SOAP-Lite-0.710.08-wfOzhM\blib\lib/SOAP/Transport/FTP.pm line 60.
t/SOAP/Transport/FTP.t ....................... ok
t/SOAP/Transport/HTTP.t ...................... ok
t/SOAP/Transport/HTTP/CGI.t ..................

everytime I get to the CGI.t at the end here the installation won't move!  Any suggestions would be greatly appreciated, I've been trying to force it through, literally for 5 hours now....

cheers,
jonny

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