[Bioperl-l] bioperl 1.6 installation on vista with perl 5.10
Chris Fields
cjfields at illinois.edu
Sat Aug 8 16:26:38 UTC 2009
Have you tried installing SOAP::Lite directly? That seems to be the
hanging point.
The funny thing is this is somehow assigning everything as a
requirement (SOAP::Lite is a 'recommends'). Worth investigating, but
I don't have access to a Windows box (either for XP, Vista, or Win7).
Hopefully we'll get a PPM up soon; it's in the roadmap for 1.6.1.
In the meantime, (as a strictly temporary measure) have you tried
setting PERL5LIB to point to a local copy of bioperl-1.6?
chris
On Aug 3, 2009, at 6:18 PM, Johnathan Dalzell wrote:
> 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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