Gbrowse 2 Errors (apparently after cpan upgrade)
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Gbrowse 2 Errors (apparently after cpan upgrade)
by joseph franklin
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Hi all,
I've had GBrowse 2.0 running fine, but I ran an upgrade in cpan yesterday to get an unrelated BioPerl module, and it broke GBrowse (or at least it happened at about the same time). Nothing else changed with the installation--no new databases or config changes. The errors are pasted below. The GBrowse version is the latest from SVN, and I've re-checked that it tests and installs fine. As you can see from the errors, I'm running it under ModPerl--I'm not sure if this has any relevance to the current situation. Can anyone with more knowledge of the server errors point me in the right direction for fixing this, whatever the cause was? Many thanks, Joe Franklin [Mon Oct 05 14:58:13 2009] [error] \n------------- EXCEPTION: Bio::Root::Exception -------------\nMSG: invalid feature line: my $feature = shift;\nSTACK: Error::throw\nSTACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm: 368\nSTACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::_make_feature /usr/ local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: 628\nSTACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::_make_indexed_feature / usr/local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/ FeatureFileLoader.pm:615\nSTACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::handle_feature /usr/ local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: 578\nSTACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::load_line / usr/local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/ FeatureFileLoader.pm:431\nSTACK: Bio::Graphics::FeatureFile::parse_data_line /usr/local/share/perl/ 5.10.0/Bio/Graphics/FeatureFile.pm:767\nSTACK: Bio::Graphics::FeatureFile::parse_line /usr/local/share/perl/5.10.0/ Bio/Graphics/FeatureFile.pm:685\nSTACK: Bio::Graphics::FeatureFile::parse_fh /usr/local/share/perl/5.10.0/Bio/ Graphics/FeatureFile.pm:636\nSTACK: Bio::Graphics::FeatureFile::parse_file /usr/local/share/perl/5.10.0/ Bio/Graphics/FeatureFile.pm:625\nSTACK: Bio::Graphics::FeatureFile::new /usr/local/share/perl/5.10.0/Bio/ Graphics/FeatureFile.pm:394\nSTACK: Bio::Graphics::Browser2::DataSource::new /usr/local/share/perl/5.10.0/ Bio/Graphics/Browser2/DataSource.pm:63\nSTACK: Bio::Graphics::Browser2::create_data_source /usr/local/share/perl/ 5.10.0/Bio/Graphics/Browser2.pm:252\nSTACK: Bio::Graphics::Browser2::Render::new /usr/local/share/perl/5.10.0/Bio/ Graphics/Browser2/Render.pm:59\nSTACK: ModPerl ::ROOT::ModPerl::Registry::usr_lib_cgi_2dbin_gb2_gbrowse::handler /usr/ lib/cgi-bin/gb2/gbrowse:33\nSTACK: ModPerl::RegistryCooker::run /usr/ lib/perl5/ModPerl/RegistryCooker.pm:204\nSTACK: ModPerl::RegistryCooker::default_handler /usr/lib/perl5/ModPerl/ RegistryCooker.pm:170\nSTACK: ModPerl::Registry::handler /usr/lib/ perl5/ModPerl/Registry.pm:31\nSTACK: -e: 0\n-----------------------------------------------------------\n ________________________________ Joe Franklin Department of Cell Biology Yale University School of Medicine 295 Congress Ave, BCMM 137 New Haven, CT 06519 USA joseph.franklin@... 407 341 3263 (cell) 203 654 7494 (google voice) ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse 2 Errors (apparently after cpan upgrade)
by Scott Cain-4
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Hi Joe,
I don't really know what is happening, but in my experience, the error "invalid feature line" frequently means there is a problem parsing a config file (I realize that's not terribly intuitive on the face of it, but so it goes for the moment). Please double check your conf file to make sure it is OK. Also, if you haven't already, restarting Apache would probably be a good idea, since the Bio::Graphics::Browser classes have been renamed to Bio::Graphics::Browser2, so there may be a problem there too. Scott On Mon, Oct 5, 2009 at 3:32 PM, joseph franklin <joseph.franklin@...> wrote: > Hi all, > > I've had GBrowse 2.0 running fine, but I ran an upgrade in cpan > yesterday to get an unrelated BioPerl module, and it broke GBrowse (or > at least it happened at about the same time). Nothing else changed > with the installation--no new databases or config changes. The errors > are pasted below. The GBrowse version is the latest from SVN, and > I've re-checked that it tests and installs fine. As you can see from > the errors, I'm running it under ModPerl--I'm not sure if this has any > relevance to the current situation. Can anyone with more knowledge of > the server errors point me in the right direction for fixing this, > whatever the cause was? > > Many thanks, > Joe Franklin > > [Mon Oct 05 14:58:13 2009] [error] \n------------- EXCEPTION: > Bio::Root::Exception -------------\nMSG: invalid feature > line: my $feature = shift;\nSTACK: Error::throw\nSTACK: > Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm: > 368\nSTACK: > Bio::DB::SeqFeature::Store::FeatureFileLoader::_make_feature /usr/ > local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: > 628\nSTACK: > Bio::DB::SeqFeature::Store::FeatureFileLoader::_make_indexed_feature / > usr/local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/ > FeatureFileLoader.pm:615\nSTACK: > Bio::DB::SeqFeature::Store::FeatureFileLoader::handle_feature /usr/ > local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: > 578\nSTACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::load_line / > usr/local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/ > FeatureFileLoader.pm:431\nSTACK: > Bio::Graphics::FeatureFile::parse_data_line /usr/local/share/perl/ > 5.10.0/Bio/Graphics/FeatureFile.pm:767\nSTACK: > Bio::Graphics::FeatureFile::parse_line /usr/local/share/perl/5.10.0/ > Bio/Graphics/FeatureFile.pm:685\nSTACK: > Bio::Graphics::FeatureFile::parse_fh /usr/local/share/perl/5.10.0/Bio/ > Graphics/FeatureFile.pm:636\nSTACK: > Bio::Graphics::FeatureFile::parse_file /usr/local/share/perl/5.10.0/ > Bio/Graphics/FeatureFile.pm:625\nSTACK: > Bio::Graphics::FeatureFile::new /usr/local/share/perl/5.10.0/Bio/ > Graphics/FeatureFile.pm:394\nSTACK: > Bio::Graphics::Browser2::DataSource::new /usr/local/share/perl/5.10.0/ > Bio/Graphics/Browser2/DataSource.pm:63\nSTACK: > Bio::Graphics::Browser2::create_data_source /usr/local/share/perl/ > 5.10.0/Bio/Graphics/Browser2.pm:252\nSTACK: > Bio::Graphics::Browser2::Render::new /usr/local/share/perl/5.10.0/Bio/ > Graphics/Browser2/Render.pm:59\nSTACK: > ModPerl > ::ROOT::ModPerl::Registry::usr_lib_cgi_2dbin_gb2_gbrowse::handler /usr/ > lib/cgi-bin/gb2/gbrowse:33\nSTACK: ModPerl::RegistryCooker::run /usr/ > lib/perl5/ModPerl/RegistryCooker.pm:204\nSTACK: > ModPerl::RegistryCooker::default_handler /usr/lib/perl5/ModPerl/ > RegistryCooker.pm:170\nSTACK: ModPerl::Registry::handler /usr/lib/ > perl5/ModPerl/Registry.pm:31\nSTACK: -e: > 0\n-----------------------------------------------------------\n > > > > ________________________________ > Joe Franklin > Department of Cell Biology > Yale University School of Medicine > 295 Congress Ave, BCMM 137 > New Haven, CT 06519 > USA > > joseph.franklin@... > 407 341 3263 (cell) > 203 654 7494 (google voice) > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9-12, 2009. Register now! > http://p.sf.net/sfu/devconf > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse 2 Errors (apparently after cpan upgrade)
by joseph franklin
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Scott,
You're right about the config file--the error is limited to one of my data sources. I'm not sure when it got changed, but I'm looking into it. Thanks again, Joe On 5 Oct 2009, at 15:41, Scott Cain wrote: > Hi Joe, > > I don't really know what is happening, but in my experience, the error > "invalid feature line" frequently means there is a problem parsing a > config file (I realize that's not terribly intuitive on the face of > it, but so it goes for the moment). Please double check your conf > file to make sure it is OK. Also, if you haven't already, restarting > Apache would probably be a good idea, since the Bio::Graphics::Browser > classes have been renamed to Bio::Graphics::Browser2, so there may be > a problem there too. > > Scott > > > On Mon, Oct 5, 2009 at 3:32 PM, joseph franklin > <joseph.franklin@...> wrote: >> Hi all, >> >> I've had GBrowse 2.0 running fine, but I ran an upgrade in cpan >> yesterday to get an unrelated BioPerl module, and it broke GBrowse >> (or >> at least it happened at about the same time). Nothing else changed >> with the installation--no new databases or config changes. The >> errors >> are pasted below. The GBrowse version is the latest from SVN, and >> I've re-checked that it tests and installs fine. As you can see from >> the errors, I'm running it under ModPerl--I'm not sure if this has >> any >> relevance to the current situation. Can anyone with more knowledge >> of >> the server errors point me in the right direction for fixing this, >> whatever the cause was? >> >> Many thanks, >> Joe Franklin >> >> [Mon Oct 05 14:58:13 2009] [error] \n------------- EXCEPTION: >> Bio::Root::Exception -------------\nMSG: invalid feature >> line: my $feature = shift;\nSTACK: Error::throw\nSTACK: >> Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm: >> 368\nSTACK: >> Bio::DB::SeqFeature::Store::FeatureFileLoader::_make_feature /usr/ >> local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: >> 628\nSTACK: >> Bio >> ::DB::SeqFeature::Store::FeatureFileLoader::_make_indexed_feature / >> usr/local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/ >> FeatureFileLoader.pm:615\nSTACK: >> Bio::DB::SeqFeature::Store::FeatureFileLoader::handle_feature /usr/ >> local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: >> 578\nSTACK: >> Bio::DB::SeqFeature::Store::FeatureFileLoader::load_line / >> usr/local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/ >> FeatureFileLoader.pm:431\nSTACK: >> Bio::Graphics::FeatureFile::parse_data_line /usr/local/share/perl/ >> 5.10.0/Bio/Graphics/FeatureFile.pm:767\nSTACK: >> Bio::Graphics::FeatureFile::parse_line /usr/local/share/perl/5.10.0/ >> Bio/Graphics/FeatureFile.pm:685\nSTACK: >> Bio::Graphics::FeatureFile::parse_fh /usr/local/share/perl/5.10.0/ >> Bio/ >> Graphics/FeatureFile.pm:636\nSTACK: >> Bio::Graphics::FeatureFile::parse_file /usr/local/share/perl/5.10.0/ >> Bio/Graphics/FeatureFile.pm:625\nSTACK: >> Bio::Graphics::FeatureFile::new /usr/local/share/perl/5.10.0/Bio/ >> Graphics/FeatureFile.pm:394\nSTACK: >> Bio::Graphics::Browser2::DataSource::new /usr/local/share/perl/ >> 5.10.0/ >> Bio/Graphics/Browser2/DataSource.pm:63\nSTACK: >> Bio::Graphics::Browser2::create_data_source /usr/local/share/perl/ >> 5.10.0/Bio/Graphics/Browser2.pm:252\nSTACK: >> Bio::Graphics::Browser2::Render::new /usr/local/share/perl/5.10.0/ >> Bio/ >> Graphics/Browser2/Render.pm:59\nSTACK: >> ModPerl >> ::ROOT::ModPerl::Registry::usr_lib_cgi_2dbin_gb2_gbrowse::handler / >> usr/ >> lib/cgi-bin/gb2/gbrowse:33\nSTACK: ModPerl::RegistryCooker::run /usr/ >> lib/perl5/ModPerl/RegistryCooker.pm:204\nSTACK: >> ModPerl::RegistryCooker::default_handler /usr/lib/perl5/ModPerl/ >> RegistryCooker.pm:170\nSTACK: ModPerl::Registry::handler /usr/lib/ >> perl5/ModPerl/Registry.pm:31\nSTACK: -e: >> 0\n-----------------------------------------------------------\n >> >> >> >> ________________________________ >> Joe Franklin >> Department of Cell Biology >> Yale University School of Medicine >> 295 Congress Ave, BCMM 137 >> New Haven, CT 06519 >> USA >> >> joseph.franklin@... >> 407 341 3263 (cell) >> 203 654 7494 (google voice) >> >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry® Developer Conference in SF, >> CA >> is the only developer event you need to attend this year. Jumpstart >> your >> developing skills, take BlackBerry mobile applications to market >> and stay >> ahead of the curve. Join us from November 9-12, 2009. Register >> now! >> http://p.sf.net/sfu/devconf >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research ________________________________ Joe Franklin Department of Cell Biology Yale University School of Medicine 295 Congress Ave, BCMM 137 New Haven, CT 06519 USA joseph.franklin@... 407 341 3263 (cell) 203 654 7494 (google voice) ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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