[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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