error for test page

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error for test page

JINGJING JIN-2
Dear all,

I have successfully installed the Gbrowse in my server.

However, when I try to test the example database in tutorial, there is some error like it cannot access the database for yeast, because it does not display gene location information.

I have checked the log file for apache in my server,

[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] GBROWSE NOTICE: To enable PDF generation, please enter the directory "/var/www" and run the commands: "sudo mkdir -p .config/inkscape .gnome2" and "sudo chown apache .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] , referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] ------------- EXCEPTION: Bio::Root::Exception -------------, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] MSG: No suitable files found in /var/lib/gbrowse2/databases/yeast_chr1+2, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Error::throw, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:486, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::IndexedBase::index_dir /usr/local/share/perl5/Bio/DB/IndexedBase.pm:444, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::IndexedBase::new /usr/local/share/perl5/Bio/DB/IndexedBase.pm:361, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::memory::commit /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:172, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:354, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:997, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::SubtrackTable::infer_settings_from_source /usr/local/lib64/perl5/Bio/Graphics/Browser2/SubtrackTable.pm:442, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::create_subtrack_manager /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:2154, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::RenderPanels::subtrack_manager /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:2270, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::RenderPanels::select_features_menu /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:1672, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::RenderPanels::wrap_rendered_track /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:649, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::scale_bar /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1065, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::render_panels /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:959, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::render_body /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:842, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::render /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:748, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:298, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: /var/www/cgi-bin/gb2/gbrowse:55, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] -----------------------------------------------------------, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/share/perl5/vendor_perl/CGI/Session/Driver/db_file.pm line 98., referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2860., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2916., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2081., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:35 2013] [error] [client 10.50.70.161] Premature end of script headers: gbrowse, referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/




However, I still cannot fix where is the problem?

Can anyone give me some suggestions?

Thanks!


Jingjing



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Re: error for test page

Scott Cain
Hi Jingjing,

The important part of the error message is "No suitable files found in /var/lib/gbrowse2/databases/yeast_chr1+2"  So the question is, if you do this on the command line:

  ls /var/lib/gbrowse2/databases/yeast_chr1+2

What do you see?

Scott



On Mon, Dec 9, 2013 at 1:51 AM, JINGJING JIN <[hidden email]> wrote:
Dear all,

I have successfully installed the Gbrowse in my server.

However, when I try to test the example database in tutorial, there is some error like it cannot access the database for yeast, because it does not display gene location information.

I have checked the log file for apache in my server,

[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] GBROWSE NOTICE: To enable PDF generation, please enter the directory "/var/www" and run the commands: "sudo mkdir -p .config/inkscape .gnome2" and "sudo chown apache .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] , referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] ------------- EXCEPTION: Bio::Root::Exception -------------, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] MSG: No suitable files found in /var/lib/gbrowse2/databases/yeast_chr1+2, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Error::throw, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:486, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::IndexedBase::index_dir /usr/local/share/perl5/Bio/DB/IndexedBase.pm:444, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::IndexedBase::new /usr/local/share/perl5/Bio/DB/IndexedBase.pm:361, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::memory::commit /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:172, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:354, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:997, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::SubtrackTable::infer_settings_from_source /usr/local/lib64/perl5/Bio/Graphics/Browser2/SubtrackTable.pm:442, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::create_subtrack_manager /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:2154, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::RenderPanels::subtrack_manager /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:2270, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::RenderPanels::select_features_menu /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:1672, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::RenderPanels::wrap_rendered_track /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:649, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::scale_bar /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1065, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::render_panels /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:959, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::render_body /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:842, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::render /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:748, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:298, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: /var/www/cgi-bin/gb2/gbrowse:55, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] -----------------------------------------------------------, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/share/perl5/vendor_perl/CGI/Session/Driver/db_file.pm line 98., referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2860., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2916., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2081., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:35 2013] [error] [client 10.50.70.161] Premature end of script headers: gbrowse, referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/




However, I still cannot fix where is the problem?

Can anyone give me some suggestions?

Thanks!


Jingjing



------------------------------------------------------------------------------
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Develop, test and display web and hybrid apps with a single code base.
Download it for free now!
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: error for test page

JINGJING JIN-2
 ls /var/lib/gbrowse2/databases/yeast_chr1+2
yeast_chr1+2.gff3


Dear scott,


I have checked the file in this folder. 

I think the file is OK.

I have also changed the authority for this folder.

It still doesn't display the test page.

Thanks!

Jingjing





On Mon, Dec 9, 2013 at 10:39 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Jingjing,

The important part of the error message is "No suitable files found in /var/lib/gbrowse2/databases/yeast_chr1+2"  So the question is, if you do this on the command line:

  ls /var/lib/gbrowse2/databases/yeast_chr1+2

What do you see?

Scott



On Mon, Dec 9, 2013 at 1:51 AM, JINGJING JIN <[hidden email]> wrote:
Dear all,

I have successfully installed the Gbrowse in my server.

However, when I try to test the example database in tutorial, there is some error like it cannot access the database for yeast, because it does not display gene location information.

I have checked the log file for apache in my server,

[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] GBROWSE NOTICE: To enable PDF generation, please enter the directory "/var/www" and run the commands: "sudo mkdir -p .config/inkscape .gnome2" and "sudo chown apache .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] , referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] ------------- EXCEPTION: Bio::Root::Exception -------------, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] MSG: No suitable files found in /var/lib/gbrowse2/databases/yeast_chr1+2, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Error::throw, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:486, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::IndexedBase::index_dir /usr/local/share/perl5/Bio/DB/IndexedBase.pm:444, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::IndexedBase::new /usr/local/share/perl5/Bio/DB/IndexedBase.pm:361, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::memory::commit /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:172, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:354, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:997, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::SubtrackTable::infer_settings_from_source /usr/local/lib64/perl5/Bio/Graphics/Browser2/SubtrackTable.pm:442, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::create_subtrack_manager /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:2154, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::RenderPanels::subtrack_manager /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:2270, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::RenderPanels::select_features_menu /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:1672, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::RenderPanels::wrap_rendered_track /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:649, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::scale_bar /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1065, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::render_panels /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:959, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::render_body /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:842, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::render /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:748, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:298, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: /var/www/cgi-bin/gb2/gbrowse:55, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] -----------------------------------------------------------, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/share/perl5/vendor_perl/CGI/Session/Driver/db_file.pm line 98., referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2860., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2916., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2081., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:35 2013] [error] [client 10.50.70.161] Premature end of script headers: gbrowse, referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/




However, I still cannot fix where is the problem?

Can anyone give me some suggestions?

Thanks!


Jingjing



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Re: error for test page

Scott Cain
Hi Jingjing,

Farther down it's complaining about not being able to create a lock file in /var/lib/gbrowse2/sessions/, so check the write permissions on that directory.  Double check that the thing in the yeast_chr1+2 directory looks like a valid GFF file (ie, that it's not just an empty or otherwise corrupted file).

Scott



On Mon, Dec 9, 2013 at 9:00 PM, jjjscuedu <[hidden email]> wrote:
 ls /var/lib/gbrowse2/databases/yeast_chr1+2
yeast_chr1+2.gff3


Dear scott,


I have checked the file in this folder. 

I think the file is OK.

I have also changed the authority for this folder.

It still doesn't display the test page.

Thanks!

Jingjing





On Mon, Dec 9, 2013 at 10:39 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Jingjing,

The important part of the error message is "No suitable files found in /var/lib/gbrowse2/databases/yeast_chr1+2"  So the question is, if you do this on the command line:

  ls /var/lib/gbrowse2/databases/yeast_chr1+2

What do you see?

Scott



On Mon, Dec 9, 2013 at 1:51 AM, JINGJING JIN <[hidden email]> wrote:
Dear all,

I have successfully installed the Gbrowse in my server.

However, when I try to test the example database in tutorial, there is some error like it cannot access the database for yeast, because it does not display gene location information.

I have checked the log file for apache in my server,

[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] GBROWSE NOTICE: To enable PDF generation, please enter the directory "/var/www" and run the commands: "sudo mkdir -p .config/inkscape .gnome2" and "sudo chown apache .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] , referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] ------------- EXCEPTION: Bio::Root::Exception -------------, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] MSG: No suitable files found in /var/lib/gbrowse2/databases/yeast_chr1+2, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Error::throw, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:486, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::IndexedBase::index_dir /usr/local/share/perl5/Bio/DB/IndexedBase.pm:444, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::IndexedBase::new /usr/local/share/perl5/Bio/DB/IndexedBase.pm:361, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::memory::commit /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:172, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:354, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:997, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::SubtrackTable::infer_settings_from_source /usr/local/lib64/perl5/Bio/Graphics/Browser2/SubtrackTable.pm:442, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::create_subtrack_manager /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:2154, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::RenderPanels::subtrack_manager /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:2270, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::RenderPanels::select_features_menu /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:1672, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::RenderPanels::wrap_rendered_track /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:649, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::scale_bar /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1065, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::render_panels /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:959, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::render_body /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:842, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::render /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:748, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:298, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] STACK: /var/www/cgi-bin/gb2/gbrowse:55, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] -----------------------------------------------------------, referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:33 2013] [error] [client 10.50.70.161] couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/share/perl5/vendor_perl/CGI/Session/Driver/db_file.pm line 98., referer: http://chuanh.tll.org.sg/gbrowse2/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2860., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2916., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:34 2013] [error] [client 10.50.70.161] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2081., referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/
[Mon Dec 09 14:35:35 2013] [error] [client 10.50.70.161] Premature end of script headers: gbrowse, referer: http://chuanh.tll.org.sg/cgi-bin/gb2/gbrowse/yeast/




However, I still cannot fix where is the problem?

Can anyone give me some suggestions?

Thanks!


Jingjing



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Re: error for test page

Raymond Wan
In reply to this post by JINGJING JIN-2

Dear Jingjing,

How about you try doing a "ls -al" to the file, instead?

The file has to be accessible by the Apache2 process and not just by your own
account.  That doesn't apply to just the file but *all* levels of directories
necessary to get to it.

That's something you should double-check...

Ray



Quoting jjjscuedu <[hidden email]>:

>  ls /var/lib/gbrowse2/databases/yeast_chr1+2
> yeast_chr1+2.gff3
>
>
> Dear scott,
>
>
> I have checked the file in this folder.
>
> I think the file is OK.
>
> I have also changed the authority for this folder.
>
> It still doesn't display the test page.
>
> Thanks!
>
> Jingjing


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Re: error for test page

Raymond Wan

Dear Jingjing,

Please continue CC'ing the mailing list so that others can help you, too!


Quoting JINGJING JIN <[hidden email]>:

> I think I have given the write permission to this folder:
>
> ls -al /var/lib/gbrowse2/databases/yeast_chr1+2/
> total 316
> drwxrwxrwx. 2 apache apache   4096 Dec  3 13:30 .
> drwxrwxrwx. 8 apache apache   4096 Dec  3 13:30 ..
> -rwxrwxrwx. 1 root   root   312303 Dec  3 13:28 yeast_chr1+2.gff3


Note that the permissions must be correct for every directory down to this file.
 That is, not just the file, but also these directories, too:

/var
/var/lib
/var/lib/gbrowse2
/var/lib/gbrowse2/databases
...

You should check this if you're still getting that error message.

And you don't need to give permissions to "other".  If you give permissions to
the user and make it owned by the "apache" process, that would be sufficient.

If you are unclear about anything above, you should look over the documentation
for Unix file permissions.  They can explain it to you better than I ever
can...  :-)

Ray




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Re: error for test page

Scott Cain
Just to be clear, you don't need to change ownership or give write permissions for the directories above gbrowse2, but you do need to give read and execute permissions to other so that the apache user (or www-data or whatever) can get directory listings and cd into those directories.

Scott


Sent from my iPad

On Dec 10, 2013, at 4:04 AM, Raymond Wan <[hidden email]> wrote:

>
> Dear Jingjing,
>
> Please continue CC'ing the mailing list so that others can help you, too!
>
>
> Quoting JINGJING JIN <[hidden email]>:
>
>> I think I have given the write permission to this folder:
>>
>> ls -al /var/lib/gbrowse2/databases/yeast_chr1+2/
>> total 316
>> drwxrwxrwx. 2 apache apache   4096 Dec  3 13:30 .
>> drwxrwxrwx. 8 apache apache   4096 Dec  3 13:30 ..
>> -rwxrwxrwx. 1 root   root   312303 Dec  3 13:28 yeast_chr1+2.gff3
>
>
> Note that the permissions must be correct for every directory down to this file.
> That is, not just the file, but also these directories, too:
>
> /var
> /var/lib
> /var/lib/gbrowse2
> /var/lib/gbrowse2/databases
> ...
>
> You should check this if you're still getting that error message.
>
> And you don't need to give permissions to "other".  If you give permissions to
> the user and make it owned by the "apache" process, that would be sufficient.
>
> If you are unclear about anything above, you should look over the documentation
> for Unix file permissions.  They can explain it to you better than I ever
> can...  :-)
>
> Ray
>
>
>
>
> -------------------------------------------------
> This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk
>
>
> ------------------------------------------------------------------------------
> Sponsored by Intel(R) XDK
> Develop, test and display web and hybrid apps with a single code base.
> Download it for free now!
> http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
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Re: error for test page

JINGJING JIN-2
Dear scoot,

Thanks for your suggestion.

I have tried to reinstall Gbrowse in my server.

Even at the test stages, some similar error is existing:

[ns_phd10@tll-yejianlab GBrowse]$ perl Build.PL 
WARNING: the following files are missing in your kit:
        lib/Bio/DB/SeqFeature/Store/LoadHelper.pm
        META.json
        META.yml
Please inform the author.

**** WARNING *****************************************************************************************
If you are upgrading from an earlier version of GBrowse and wish to use named user accounts, please 
set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run bin/gbrowse_metadb_config.pl to 
create/update your user account database.

See /etc/gbrowse2/GBrowse.conf.new for suggested settings.
******************************************************************************************************
**** WARNING *********************************************************
You appear to have SELinux installed on this computer. This can
interfere with GBrowse operation. Please read the file
README.fedora_and_selinux in order to perform additional configuration
operations that may be necessary to run on this computer.
**********************************************************************
Created MYMETA.yml and MYMETA.json






[ns_phd10@tll-yejianlab GBrowse]$ ./Build test 
NOTE: Run ./Build reconfig to change existing configuration.
/etc/httpd/conf.d/gbrowse2.conf is already installed. Please run ./Build apache_conf to see this file's recommended contents.
t/00.compile.t ............ ok     
t/01.yeast.t .............. 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: No suitable files found in /home/ns_phd10/GBrowse/t/../sample_data/yeast_chr1+2
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:486
STACK: Bio::DB::IndexedBase::index_dir /usr/local/share/perl5/Bio/DB/IndexedBase.pm:444
STACK: Bio::DB::IndexedBase::new /usr/local/share/perl5/Bio/DB/IndexedBase.pm:361
STACK: Bio::DB::SeqFeature::Store::memory::commit /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:172
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352
STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:354
STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243
STACK: Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164
STACK: Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395
STACK: t/01.yeast.t:26
-----------------------------------------------------------



I am not sure about these Exception.

Can you give me some suggestions?

Thanks!

Jingjing




On Wed, Dec 11, 2013 at 12:53 AM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Just to be clear, you don't need to change ownership or give write permissions for the directories above gbrowse2, but you do need to give read and execute permissions to other so that the apache user (or www-data or whatever) can get directory listings and cd into those directories.

Scott


Sent from my iPad

On Dec 10, 2013, at 4:04 AM, Raymond Wan <[hidden email]> wrote:

>
> Dear Jingjing,
>
> Please continue CC'ing the mailing list so that others can help you, too!
>
>
> Quoting JINGJING JIN <[hidden email]>:

>
>> I think I have given the write permission to this folder:
>>
>> ls -al /var/lib/gbrowse2/databases/yeast_chr1+2/
>> total 316
>> drwxrwxrwx. 2 apache apache   4096 Dec  3 13:30 .
>> drwxrwxrwx. 8 apache apache   4096 Dec  3 13:30 ..
>> -rwxrwxrwx. 1 root   root   312303 Dec  3 13:28 yeast_chr1+2.gff3
>
>
> Note that the permissions must be correct for every directory down to this file.
> That is, not just the file, but also these directories, too:
>
> /var
> /var/lib
> /var/lib/gbrowse2
> /var/lib/gbrowse2/databases
> ...
>
> You should check this if you're still getting that error message.
>
> And you don't need to give permissions to "other".  If you give permissions to
> the user and make it owned by the "apache" process, that would be sufficient.
>
> If you are unclear about anything above, you should look over the documentation
> for Unix file permissions.  They can explain it to you better than I ever
> can...  :-)
>
> Ray
>
>
>
>
> -------------------------------------------------
> This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk
>
>
> ------------------------------------------------------------------------------
> Sponsored by Intel(R) XDK
> Develop, test and display web and hybrid apps with a single code base.
> Download it for free now!
> http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

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