Questions on installing Bioperl
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Questions on installing Bioperl
by Dr. W Mao
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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@...>', ...) 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 _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: Questions on installing Bioperl
by Chris Fields-5
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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@...>', ...) 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 > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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