[Bioperl-l] Questions on installing Bioperl

[Chris Fields]

The last two paragraphs from the CPAN error indicate the problem,  
namely you need to configure the urllist parameter (it's not a bioperl  
problem).  The instructions there are pretty explicit:

> You have not configured a urllist and do not allow connections to the
> internet to get a list of mirrors.  If you wish to get a list of CPAN
> mirrors to pick from, use this command
>     o conf init connect_to_internet_ok urllist
> If you do not wish to get a list of mirrors and would prefer to set
> your urllist manually, use just this command instead
>     o conf init urllist


chris


On Oct 4, 2009, at 10:43 AM, Dr. W Mao wrote:

> Hello,
>    I tried to use the >perl Build.PL to install it and I got the  
> fllowing message. I can't run >./Build test. Could you please tell  
> me waht's going on here? Thanks.
>
>
>
>
> Checking whether your kit is complete...
> Looks good
> Checking prerequisites...
>  - ERROR: IO::String is not installed
> CPAN: File::HomeDir loaded ok (v0.86)
> (I think you ran Build.PL directly, so will use CPAN to install  
> prerequisites on demand)
> CPAN: Storable loaded ok (v2.15)
> Going to read '/root/.cpan/Metadata'
>   Database was generated on Sun, 04 Oct 2009 11:27:07 GMT
> Running install for module 'IO::String'
> Running make for G/GA/GAAS/IO-String-1.08.tar.gz
> CPAN: LWP::UserAgent loaded ok (v2.033)
> CPAN: Time::HiRes loaded ok (v1.9715)
> Warning: no success downloading '/root/.cpan/sources/authors/id/G/GA/ 
> GAAS/IO-String-1.08.tar.gz.tmp28623'. Giving up on it. at /usr/lib/ 
> perl5/5.8.8/CPAN/FTP.pm line 837
>         CPAN::FTP::hostdlhard('CPAN::FTP', 'ARRAY(0x76f0030)',  
> 'authors/id/G/GA/GAAS/IO-String-1.08.tar.gz', '/root/.cpan/sources/ 
> authors/id/G/GA/GAAS/IO-String-1.08.tar.g...', 'HASH(0xdaa5a10)')  
> called at /usr/lib/perl5/5.8.8/CPAN/FTP.pm line 515
>         CPAN::FTP::hostdlxxx('CPAN::FTP', 'dlhard', 'undef', 'ARRAY 
> (0x76f0030)', 'authors/id/G/GA/GAAS/IO-String-1.08.tar.gz', '/ 
> root/.cpan/sources/authors/id/G/GA/GAAS/IO-String-1.08.tar.g...',  
> 'HASH(0xdaa5a10)') called at /usr/lib/perl5/5.8.8/CPAN/FTP.pm line 442
>         CPAN::FTP::localize('CPAN::FTP', 'authors/id/G/GA/GAAS/IO- 
> String-1.08.tar.gz', '/root/.cpan/sources/authors/id/G/GA/GAAS/IO- 
> String-1.08.tar.gz') called at /usr/lib/perl5/5.8.8/CPAN/ 
> Distribution.pm line 379
>         CPAN::Distribution::get_file_onto_local_disk 
> ('CPAN::Distribution=HASH(0xd65ddb0)') called at /usr/lib/ 
> perl5/5.8.8/CPAN/Distribution.pm line 343
>         CPAN::Distribution::get('CPAN::Distribution=HASH 
> (0xd65ddb0)') called at /usr/lib/perl5/5.8.8/CPAN/Distribution.pm  
> line 1677
>         CPAN::Distribution::make('CPAN::Distribution=HASH 
> (0xd65ddb0)') called at /usr/lib/perl5/5.8.8/CPAN/Distribution.pm  
> line 2876
>         CPAN::Distribution::test('CPAN::Distribution=HASH 
> (0xd65ddb0)') called at /usr/lib/perl5/5.8.8/CPAN/Distribution.pm  
> line 3266
>         CPAN::Distribution::install('CPAN::Distribution=HASH 
> (0xd65ddb0)') called at /usr/lib/perl5/5.8.8/CPAN/Module.pm line 474
>         eval {...} called at /usr/lib/perl5/5.8.8/CPAN/Module.pm  
> line 473
>         CPAN::Module::rematein('CPAN::Module=HASH(0xb5e0af0)',  
> 'install') called at /usr/lib/perl5/5.8.8/CPAN/Module.pm line 576
>         CPAN::Module::install('CPAN::Module=HASH(0xb5e0af0)') called  
> at /usr/lib/perl5/5.8.8/CPAN/Shell.pm line 1755
>         CPAN::Shell::rematein('CPAN::Shell', 'install',  
> 'IO::String') called at /usr/lib/perl5/5.8.8/CPAN/Shell.pm line 1935
>         CPAN::Shell::__ANON__('CPAN::Shell', 'IO::String') called at  
> Bio/Root/Build.pm line 449
>         Bio::Root::Build::install_prereq('Bio::Root::Build=HASH 
> (0x7104900)', 'IO::String', 0) called at Bio/Root/Build.pm line 473
>         Bio::Root::Build::install_required('Bio::Root::Build=HASH 
> (0x7104900)', 'IO::String', 0, 'IO::String is not installed') called  
> at Bio/Root/Build.pm line 414
>         Bio::Root::Build::prereq_failures('Bio::Root::Build=HASH 
> (0x7104900)', 'HASH(0x6e02b40)') called at /usr/lib/perl5/site_perl/ 
> 5.8.8/Module/Build/Base.pm line 1270
>         Module::Build::Base::check_prereq('Bio::Root::Build=HASH 
> (0x7104900)') called at /usr/lib/perl5/site_perl/5.8.8/Module/Build/ 
> Base.pm line 39
>         Module::Build::Base::new('Bio::Root::Build', 'module_name',  
> 'Bio', 'dist_name', 'BioPerl', 'dist_version_from', 'Bio/Root/ 
> Version.pm', 'dist_author', 'BioPerl Team <bioperl- 
> l at bioperl.org>', ...) called at Build.PL line 21
>
> You have not configured a urllist and do not allow connections to the
> internet to get a list of mirrors.  If you wish to get a list of CPAN
> mirrors to pick from, use this command
>     o conf init connect_to_internet_ok urllist
> If you do not wish to get a list of mirrors and would prefer to set
> your urllist manually, use just this command instead
>     o conf init urllist
>
>
>
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