Getting a high-resolution image and its PDF in GBrowse 2
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Getting a high-resolution image and its PDF in GBrowse 2
by Erick Antezana-4
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Hello,
I have just updated my Bioperl install (live version). I tried to test the generation of a high-resolution image (by clicking on the link found in the header of the browser) and I got the following Apache error message (see full error log messages at the end of this email): Can't locate object method "create_cookie" via package "Bio::Graphics::Browser::Render" at ...../cgi-bin/gbrowse_img line 112. There seems to be a non-implemented subroutine? Some more info: GD version: 2.44 GD::SVG version 0.33 libgd version 2.0.33 On the other hand, I have also tried to get an image in PDF ([Download PDF] link) and I got the same error message as above (see full log at the end of this email) but with some more details about some non-implemented-yet subroutines (e.g. clip, saveAlpha, alphaBlending). Any suggestions? Erick p.s.1. Error log while trying to retrieve a high-res image [error] Useless use of a constant in void context at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] [14433] RUN(): GET: http://erick/cgi-bin/gbrowse/yeast/ make_image=GD%3A%3ASVG at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 147., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] event(make_image) at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 266., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] Use of uninitialized value $mime_type in concatenation (.) or string at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] [14433] asynchronous event returning status=302, mime-type= at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] [14433] asynchronous exit at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 162., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] Useless use of a constant in void context at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] init() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 209., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] set_default_state() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 210., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] init_database() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 212., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] init_plugins() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 214., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] init_remote_sources() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 216., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] initializing uploaded files... at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm line 20., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] add_files_from_state() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm line 35., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] name_file() returns => (file:foo,/data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo) at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UserData.pm line 127., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] @@@ /data/tmp/tmp_apache/userdata/yeast/uploads/erick/, referer: http://erick/cgi-bin/gbrowse/yeast/ [error] init done at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 218., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] [14434] update_state() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 1909., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] [14434] CGI updated at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 1916., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] [14434] update_state() done at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 1932., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] FEATURESET = Bio::Graphics::Browser::PluginSet=HASH(0x45a9a90), sources = at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] FEATURESET = Bio::Graphics::Browser::UploadSet=HASH(0x500ac00), sources = at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] FEATURESET = Bio::Graphics::Browser::RemoteSet=HASH(0x500ac48), sources = at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] FEATURE files = at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 3502., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] Can't locate object method "create_cookie" via package "Bio::Graphics::Browser::Render" at /tools/bioinfo/apache/cgi-bin/Tools/GeneticAndGenomic/GGB/gbrowse_img line 112., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] Premature end of script headers: gbrowse_img, referer: http://erick/cgi-bin/gbrowse/yeast/ p.s.2. Error log while asking for an image in PDF format: [error] Useless use of a constant in void context at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] [14736] RUN(): GET: http://erick/cgi-bin/gbrowse/yeast/ make_image=PDF at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 147., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] event(make_image) at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 266., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] Use of uninitialized value $mime_type in concatenation (.) or string at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] [14736] asynchronous event returning status=302, mime-type= at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] [14736] asynchronous exit at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 162., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] Useless use of a constant in void context at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] init() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 209., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] set_default_state() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 210., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] init_database() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 212., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] init_plugins() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 214., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] init_remote_sources() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 216., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] initializing uploaded files... at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm line 20., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] add_files_from_state() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm line 35., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] /data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo, referer: http://erick/cgi-bin/gbrowse/yeast/ [error] name_file() returns => (file:foo,/data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo) at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UserData.pm line 127., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] @@@ /data/tmp/tmp_apache/userdata/yeast/uploads/erick/, referer: http://erick/cgi-bin/gbrowse/yeast/ [error] init done at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 218., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] [14737] update_state() at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 1909., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] [14737] CGI updated at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 1916., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] [14737] update_state() done at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 1932., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] FEATURESET = Bio::Graphics::Browser::PluginSet=HASH(0x1e655d60), sources = at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] FEATURESET = Bio::Graphics::Browser::UploadSet=HASH(0x1f0adc30), sources = at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] FEATURESET = Bio::Graphics::Browser::RemoteSet=HASH(0x1f0adc78), sources = at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] FEATURE files = at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm line 3502., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method saveAlpha is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method alphaBlending is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method fill is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method alphaBlending is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method saveAlpha is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method alphaBlending is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method fill is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method alphaBlending is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method saveAlpha is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method alphaBlending is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method fill is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method alphaBlending is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method saveAlpha is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method alphaBlending is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method fill is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method alphaBlending is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method saveAlpha is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method alphaBlending is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method fill is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method alphaBlending is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] GD method clip is not implemented in GD::SVG at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] Can't locate object method "create_cookie" via package "Bio::Graphics::Browser::Render" at /tools/bioinfo/apache/cgi-bin/Tools/GeneticAndGenomic/GGB/gbrowse_img line 112., referer: http://erick/cgi-bin/gbrowse/yeast/ [error] Premature end of script headers: gbrowse_img, referer: http://erick/cgi-bin/gbrowse/yeast/ ------------------------------------------------------------------------------ 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: Getting a high-resolution image and its PDF in GBrowse 2
by Lincoln Stein-3
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Hi Erick,
I'm sorry about this. I'll have to release a patch to GBrowse 1.7. Lincoln On Mon, Oct 5, 2009 at 9:37 AM, Erick Antezana <erick.antezana@...> wrote: Hello, -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ 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: Getting a high-resolution image and its PDF in GBrowse 2
by Lincoln Stein-3
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Erick, is this happening in GBrowse 1.7 or 2.0?
Lincoln On Mon, Oct 5, 2009 at 9:37 AM, Erick Antezana <erick.antezana@...> wrote: Hello, -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ 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: Getting a high-resolution image and its PDF in GBrowse 2
by Erick Antezana-4
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Lincoln,
it is happening in GBrowse 2.0 thanks, Erick 2009/10/5 Lincoln Stein <lincoln.stein@...> Erick, is this happening in GBrowse 1.7 or 2.0? ------------------------------------------------------------------------------ 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: Getting a high-resolution image and its PDF in GBrowse 2
by Lincoln Stein-3
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Hi Erick,
Could you do an SVN update to pick up the fix? If you are not comfortable with that I'll release a new version to CPAN tomorrow. Lincoln On Mon, Oct 5, 2009 at 2:54 PM, Erick Antezana <erick.antezana@...> wrote: Lincoln, -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ 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: Getting a high-resolution image and its PDF in GBrowse 2
by Erick Antezana-4
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Hi Lincoln,
I have just SVN-updated my GBrowse install. After launching the command "Build test", I got a few warning and error messages: t/02.rearchitecture.t ..... 1/90 Use of uninitialized value $dbid in hash element at /home/user/Generic-Genome-Browser/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 530. .... Can't locate object method "add_user_type" via package "Bio::Graphics::Browser2::DataSource" at t/02.rearchitecture.t line 263. t/02.rearchitecture.t ..... Dubious, test returned 255 (wstat 65280, 0xff00) .... t/03.render.t ............. 123/148 Can't locate object method "delete_track" via package "Bio::Graphics::Browser2::UserTracks" at t/03.render.t line 496. t/03.render.t ............. Dubious, test returned 255 (wstat 65280, 0xff00) I will come back to you later with the result of the tests regarding th high-res image generation. thanks, Erick 2009/10/5 Lincoln Stein <lincoln.stein@...> Hi Erick, ------------------------------------------------------------------------------ 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: Getting a high-resolution image and its PDF in GBrowse 2
by Lincoln Stein-3
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Sorry about the regression test failures. This will be fixed sometime today.
Lincoln On Tue, Oct 6, 2009 at 5:03 AM, Erick Antezana <erick.antezana@...> wrote: Hi Lincoln, -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ 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: Getting a high-resolution image and its PDF in GBrowse 2
by Erick Antezana-4
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Hi Lincoln,
I have just SVN-updated my GBrowse 2 install. The high-res image generations works fine. However, the PDF generation is still broken :-( Could you please take a look at it? On the other hand, we were wondering whether the 'High-res Image' should actually display (generate) an image of the actual tracks layout that are displayed? The GBrowse 2.0 interface (AJAX-based) allows users to move tracks (which is very useful) and stack them into various ways (change_track_order). Nevertheless, if we move any track and then click on 'High-res Image', we get an image displaying the initial layout and not the one resulting after making some moves :-( Would that be possible to have? I have realised that the directory (modules) ...../Bio/Graphics/Browser has been renamed to ...../Bio/Graphics/Browser2 , is it still needed to cascade this renaming in the plugin "Reporter.pm"? Finally, the regression test are still reporting the same failures as reported recently. thanks again, Erick 2009/10/6 Lincoln Stein <lincoln.stein@...>: > Sorry about the regression test failures. This will be fixed sometime today. > > Lincoln > > On Tue, Oct 6, 2009 at 5:03 AM, Erick Antezana <erick.antezana@...> > wrote: >> >> Hi Lincoln, >> >> I have just SVN-updated my GBrowse install. After launching the command >> "Build test", I got a few warning and error messages: >> >> >> t/02.rearchitecture.t ..... 1/90 Use of uninitialized value $dbid in hash >> element at >> /home/user/Generic-Genome-Browser/t/../lib/Bio/Graphics/Browser2/DataSource.pm >> line 530. >> >> .... >> >> Can't locate object method "add_user_type" via package >> "Bio::Graphics::Browser2::DataSource" at t/02.rearchitecture.t line 263. >> t/02.rearchitecture.t ..... Dubious, test returned 255 (wstat 65280, >> 0xff00) >> >> >> .... >> >> t/03.render.t ............. 123/148 Can't locate object method >> "delete_track" via package "Bio::Graphics::Browser2::UserTracks" at >> t/03.render.t line 496. >> t/03.render.t ............. Dubious, test returned 255 (wstat 65280, >> 0xff00) >> >> >> I will come back to you later with the result of the tests regarding th >> high-res image generation. >> >> thanks, >> Erick >> >> 2009/10/5 Lincoln Stein <lincoln.stein@...> >>> >>> Hi Erick, >>> >>> Could you do an SVN update to pick up the fix? If you are not comfortable >>> with that I'll release a new version to CPAN tomorrow. >>> >>> Lincoln >>> >>> On Mon, Oct 5, 2009 at 2:54 PM, Erick Antezana <erick.antezana@...> >>> wrote: >>>> >>>> Lincoln, >>>> >>>> it is happening in GBrowse 2.0 >>>> >>>> thanks, >>>> Erick >>>> >>>> 2009/10/5 Lincoln Stein <lincoln.stein@...> >>>>> >>>>> Erick, is this happening in GBrowse 1.7 or 2.0? >>>>> >>>>> Lincoln >>>>> >>>>> On Mon, Oct 5, 2009 at 9:37 AM, Erick Antezana >>>>> <erick.antezana@...> wrote: >>>>>> >>>>>> Hello, >>>>>> >>>>>> I have just updated my Bioperl install (live version). I tried to >>>>>> test the generation of a high-resolution image (by clicking on the link >>>>>> found in the header of the browser) and I got the following Apache error >>>>>> message (see full error log messages at the end of this email): >>>>>> >>>>>> Can't locate object method "create_cookie" via package >>>>>> "Bio::Graphics::Browser::Render" at ...../cgi-bin/gbrowse_img line 112. >>>>>> >>>>>> There seems to be a non-implemented subroutine? >>>>>> >>>>>> Some more info: >>>>>> >>>>>> GD version: 2.44 >>>>>> GD::SVG version 0.33 >>>>>> libgd version 2.0.33 >>>>>> >>>>>> >>>>>> On the other hand, I have also tried to get an image in PDF ([Download >>>>>> PDF] link) and I got the same error message as above (see full log at the >>>>>> end of this email) but with some more details about some non-implemented-yet >>>>>> subroutines (e.g. clip, saveAlpha, alphaBlending). >>>>>> >>>>>> Any suggestions? >>>>>> Erick >>>>>> >>>>>> p.s.1. Error log while trying to retrieve a high-res image >>>>>> >>>>>> [error] Useless use of a constant in void context at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] [14433] RUN(): GET: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> make_image=GD%3A%3ASVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 147., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] event(make_image) at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 266., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] Use of uninitialized value $mime_type in concatenation (.) or >>>>>> string at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] [14433] asynchronous event returning status=302, mime-type= >>>>>> at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] [14433] asynchronous exit at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 162., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] Useless use of a constant in void context at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] init() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 209., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] set_default_state() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 210., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] init_database() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 212., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] init_plugins() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 214., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] init_remote_sources() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 216., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] initializing uploaded files... at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >>>>>> line 20., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] add_files_from_state() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >>>>>> line 35., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] name_file() returns => >>>>>> (file:foo,/data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo) at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UserData.pm >>>>>> line 127., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] @@@ /data/tmp/tmp_apache/userdata/yeast/uploads/erick/, >>>>>> referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] init done at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 218., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] [14434] update_state() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 1909., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] [14434] CGI updated at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 1916., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] [14434] update_state() done at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 1932., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] FEATURESET = >>>>>> Bio::Graphics::Browser::PluginSet=HASH(0x45a9a90), sources = at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] FEATURESET = >>>>>> Bio::Graphics::Browser::UploadSet=HASH(0x500ac00), sources = at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] FEATURESET = >>>>>> Bio::Graphics::Browser::RemoteSet=HASH(0x500ac48), sources = at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] FEATURE files = at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 3502., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] Can't locate object method "create_cookie" via package >>>>>> "Bio::Graphics::Browser::Render" at >>>>>> /tools/bioinfo/apache/cgi-bin/Tools/GeneticAndGenomic/GGB/gbrowse_img line >>>>>> 112., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] Premature end of script headers: gbrowse_img, referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> p.s.2. Error log while asking for an image in PDF format: >>>>>> >>>>>> [error] Useless use of a constant in void context at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] [14736] RUN(): GET: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> make_image=PDF at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 147., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] event(make_image) at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 266., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] Use of uninitialized value $mime_type in concatenation (.) or >>>>>> string at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] [14736] asynchronous event returning status=302, mime-type= >>>>>> at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] [14736] asynchronous exit at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 162., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] Useless use of a constant in void context at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] init() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 209., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] set_default_state() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 210., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] init_database() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 212., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] init_plugins() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 214., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] init_remote_sources() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 216., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] initializing uploaded files... at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >>>>>> line 20., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] add_files_from_state() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >>>>>> line 35., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] /data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo, >>>>>> referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] name_file() returns => >>>>>> (file:foo,/data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo) at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UserData.pm >>>>>> line 127., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] @@@ /data/tmp/tmp_apache/userdata/yeast/uploads/erick/, >>>>>> referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] init done at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 218., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] [14737] update_state() at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 1909., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] [14737] CGI updated at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 1916., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] [14737] update_state() done at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 1932., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] FEATURESET = >>>>>> Bio::Graphics::Browser::PluginSet=HASH(0x1e655d60), sources = at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] FEATURESET = >>>>>> Bio::Graphics::Browser::UploadSet=HASH(0x1f0adc30), sources = at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] FEATURESET = >>>>>> Bio::Graphics::Browser::RemoteSet=HASH(0x1f0adc78), sources = at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] FEATURE files = at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>> line 3502., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] Can't locate object method "create_cookie" via package >>>>>> "Bio::Graphics::Browser::Render" at >>>>>> /tools/bioinfo/apache/cgi-bin/Tools/GeneticAndGenomic/GGB/gbrowse_img line >>>>>> 112., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>> [error] Premature end of script headers: gbrowse_img, referer: >>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> 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 >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Lincoln D. Stein >>>>> Director, Informatics and Biocomputing Platform >>>>> Ontario Institute for Cancer Research >>>>> 101 College St., Suite 800 >>>>> Toronto, ON, Canada M5G0A3 >>>>> 416 673-8514 >>>>> Assistant: Renata Musa <Renata.Musa@...> >>>> >>> >>> >>> >>> -- >>> Lincoln D. Stein >>> Director, Informatics and Biocomputing Platform >>> Ontario Institute for Cancer Research >>> 101 College St., Suite 800 >>> Toronto, ON, Canada M5G0A3 >>> 416 673-8514 >>> Assistant: Renata Musa <Renata.Musa@...> >> > > > > -- > Lincoln D. Stein > Director, Informatics and Biocomputing Platform > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa <Renata.Musa@...> > ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) 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/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Getting a high-resolution image and its PDF in GBrowse 2
by Scott Cain-4
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Hi Lincoln and Erick,
Based on a recursive grep through the source looking for "Browser" but not "Browser2", it looks to me like the following files may still need some fixing for the Browser->Browser2 change: Build.PL: copy("./libalign/$_" => "./lib/Bio/Graphics/Browser/$_"); bin/gbrowse_clean.pl:use Bio::Graphics::Browser; bin/gbrowse_slave:use Bio::Graphics::Browser::Render::Slave; cgi-bin/gbrowse_details:use Bio::Graphics::Browser; cgi-bin/gbrowse_gmap:use Bio::Graphics::Browser; cgi-bin/gbrowse_login:use Bio::Graphics::Browser; conf/plugins/PrimerDesigner.pm:use Bio::Graphics::Browser; contrib/Coverage/plugin/Coverage.pm:use Bio::Graphics::Browser::Plugin; contrib/TextDumper/TextDumper.pm:use Bio::Graphics::Browser::Plugin; libalign/CAlign.pm:package Bio::Graphics::Browser::CAlign; libalign/CAlign.xs:_do_alignment(packname="Bio::Graphics::Browser::CAlign",src,tgt,options=NULL) Scott On Wed, Oct 7, 2009 at 10:03 AM, Erick Antezana <erick.antezana@...> wrote: > Hi Lincoln, > > I have just SVN-updated my GBrowse 2 install. The high-res image > generations works fine. However, the PDF generation is still broken > :-( Could you please take a look at it? > > On the other hand, we were wondering whether the 'High-res Image' > should actually display (generate) an image of the actual tracks > layout that are displayed? The GBrowse 2.0 interface (AJAX-based) > allows users to move tracks (which is very useful) and stack them into > various ways (change_track_order). Nevertheless, if we move any track > and then click on 'High-res Image', we get an image displaying the > initial layout and not the one resulting after making some moves :-( > Would that be possible to have? > > I have realised that the directory (modules) > ...../Bio/Graphics/Browser has been renamed to > ...../Bio/Graphics/Browser2 , is it still needed to cascade this > renaming in the plugin "Reporter.pm"? > > Finally, the regression test are still reporting the same failures > as reported recently. > > thanks again, > Erick > > 2009/10/6 Lincoln Stein <lincoln.stein@...>: >> Sorry about the regression test failures. This will be fixed sometime today. >> >> Lincoln >> >> On Tue, Oct 6, 2009 at 5:03 AM, Erick Antezana <erick.antezana@...> >> wrote: >>> >>> Hi Lincoln, >>> >>> I have just SVN-updated my GBrowse install. After launching the command >>> "Build test", I got a few warning and error messages: >>> >>> >>> t/02.rearchitecture.t ..... 1/90 Use of uninitialized value $dbid in hash >>> element at >>> /home/user/Generic-Genome-Browser/t/../lib/Bio/Graphics/Browser2/DataSource.pm >>> line 530. >>> >>> .... >>> >>> Can't locate object method "add_user_type" via package >>> "Bio::Graphics::Browser2::DataSource" at t/02.rearchitecture.t line 263. >>> t/02.rearchitecture.t ..... Dubious, test returned 255 (wstat 65280, >>> 0xff00) >>> >>> >>> .... >>> >>> t/03.render.t ............. 123/148 Can't locate object method >>> "delete_track" via package "Bio::Graphics::Browser2::UserTracks" at >>> t/03.render.t line 496. >>> t/03.render.t ............. Dubious, test returned 255 (wstat 65280, >>> 0xff00) >>> >>> >>> I will come back to you later with the result of the tests regarding th >>> high-res image generation. >>> >>> thanks, >>> Erick >>> >>> 2009/10/5 Lincoln Stein <lincoln.stein@...> >>>> >>>> Hi Erick, >>>> >>>> Could you do an SVN update to pick up the fix? If you are not comfortable >>>> with that I'll release a new version to CPAN tomorrow. >>>> >>>> Lincoln >>>> >>>> On Mon, Oct 5, 2009 at 2:54 PM, Erick Antezana <erick.antezana@...> >>>> wrote: >>>>> >>>>> Lincoln, >>>>> >>>>> it is happening in GBrowse 2.0 >>>>> >>>>> thanks, >>>>> Erick >>>>> >>>>> 2009/10/5 Lincoln Stein <lincoln.stein@...> >>>>>> >>>>>> Erick, is this happening in GBrowse 1.7 or 2.0? >>>>>> >>>>>> Lincoln >>>>>> >>>>>> On Mon, Oct 5, 2009 at 9:37 AM, Erick Antezana >>>>>> <erick.antezana@...> wrote: >>>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I have just updated my Bioperl install (live version). I tried to >>>>>>> test the generation of a high-resolution image (by clicking on the link >>>>>>> found in the header of the browser) and I got the following Apache error >>>>>>> message (see full error log messages at the end of this email): >>>>>>> >>>>>>> Can't locate object method "create_cookie" via package >>>>>>> "Bio::Graphics::Browser::Render" at ...../cgi-bin/gbrowse_img line 112. >>>>>>> >>>>>>> There seems to be a non-implemented subroutine? >>>>>>> >>>>>>> Some more info: >>>>>>> >>>>>>> GD version: 2.44 >>>>>>> GD::SVG version 0.33 >>>>>>> libgd version 2.0.33 >>>>>>> >>>>>>> >>>>>>> On the other hand, I have also tried to get an image in PDF ([Download >>>>>>> PDF] link) and I got the same error message as above (see full log at the >>>>>>> end of this email) but with some more details about some non-implemented-yet >>>>>>> subroutines (e.g. clip, saveAlpha, alphaBlending). >>>>>>> >>>>>>> Any suggestions? >>>>>>> Erick >>>>>>> >>>>>>> p.s.1. Error log while trying to retrieve a high-res image >>>>>>> >>>>>>> [error] Useless use of a constant in void context at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] [14433] RUN(): GET: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> make_image=GD%3A%3ASVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 147., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] event(make_image) at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 266., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] Use of uninitialized value $mime_type in concatenation (.) or >>>>>>> string at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] [14433] asynchronous event returning status=302, mime-type= >>>>>>> at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] [14433] asynchronous exit at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 162., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] Useless use of a constant in void context at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] init() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 209., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] set_default_state() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 210., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] init_database() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 212., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] init_plugins() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 214., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] init_remote_sources() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 216., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] initializing uploaded files... at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >>>>>>> line 20., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] add_files_from_state() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >>>>>>> line 35., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] name_file() returns => >>>>>>> (file:foo,/data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo) at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UserData.pm >>>>>>> line 127., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] @@@ /data/tmp/tmp_apache/userdata/yeast/uploads/erick/, >>>>>>> referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] init done at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 218., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] [14434] update_state() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 1909., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] [14434] CGI updated at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 1916., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] [14434] update_state() done at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 1932., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] FEATURESET = >>>>>>> Bio::Graphics::Browser::PluginSet=HASH(0x45a9a90), sources = at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] FEATURESET = >>>>>>> Bio::Graphics::Browser::UploadSet=HASH(0x500ac00), sources = at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] FEATURESET = >>>>>>> Bio::Graphics::Browser::RemoteSet=HASH(0x500ac48), sources = at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] FEATURE files = at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 3502., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] Can't locate object method "create_cookie" via package >>>>>>> "Bio::Graphics::Browser::Render" at >>>>>>> /tools/bioinfo/apache/cgi-bin/Tools/GeneticAndGenomic/GGB/gbrowse_img line >>>>>>> 112., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] Premature end of script headers: gbrowse_img, referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> p.s.2. Error log while asking for an image in PDF format: >>>>>>> >>>>>>> [error] Useless use of a constant in void context at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] [14736] RUN(): GET: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> make_image=PDF at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 147., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] event(make_image) at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 266., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] Use of uninitialized value $mime_type in concatenation (.) or >>>>>>> string at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] [14736] asynchronous event returning status=302, mime-type= >>>>>>> at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] [14736] asynchronous exit at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 162., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] Useless use of a constant in void context at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] init() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 209., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] set_default_state() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 210., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] init_database() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 212., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] init_plugins() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 214., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] init_remote_sources() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 216., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] initializing uploaded files... at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >>>>>>> line 20., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] add_files_from_state() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >>>>>>> line 35., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] /data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo, >>>>>>> referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] name_file() returns => >>>>>>> (file:foo,/data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo) at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UserData.pm >>>>>>> line 127., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] @@@ /data/tmp/tmp_apache/userdata/yeast/uploads/erick/, >>>>>>> referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] init done at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 218., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] [14737] update_state() at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 1909., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] [14737] CGI updated at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 1916., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] [14737] update_state() done at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 1932., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] FEATURESET = >>>>>>> Bio::Graphics::Browser::PluginSet=HASH(0x1e655d60), sources = at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] FEATURESET = >>>>>>> Bio::Graphics::Browser::UploadSet=HASH(0x1f0adc30), sources = at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] FEATURESET = >>>>>>> Bio::Graphics::Browser::RemoteSet=HASH(0x1f0adc78), sources = at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] FEATURE files = at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>> line 3502., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] Can't locate object method "create_cookie" via package >>>>>>> "Bio::Graphics::Browser::Render" at >>>>>>> /tools/bioinfo/apache/cgi-bin/Tools/GeneticAndGenomic/GGB/gbrowse_img line >>>>>>> 112., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> [error] Premature end of script headers: gbrowse_img, referer: >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> 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 >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Lincoln D. Stein >>>>>> Director, Informatics and Biocomputing Platform >>>>>> Ontario Institute for Cancer Research >>>>>> 101 College St., Suite 800 >>>>>> Toronto, ON, Canada M5G0A3 >>>>>> 416 673-8514 >>>>>> Assistant: Renata Musa <Renata.Musa@...> >>>>> >>>> >>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> Director, Informatics and Biocomputing Platform >>>> Ontario Institute for Cancer Research >>>> 101 College St., Suite 800 >>>> Toronto, ON, Canada M5G0A3 >>>> 416 673-8514 >>>> Assistant: Renata Musa <Renata.Musa@...> >>> >> >> >> >> -- >> Lincoln D. Stein >> Director, Informatics and Biocomputing Platform >> Ontario Institute for Cancer Research >> 101 College St., Suite 800 >> Toronto, ON, Canada M5G0A3 >> 416 673-8514 >> Assistant: Renata Musa <Renata.Musa@...> >> > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) 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/devconference > _______________________________________________ > 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(R) 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/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Getting a high-resolution image and its PDF in GBrowse 2
by Lincoln Stein-3
::
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Hi Scott,
Thanks so much for finding these things. I'll work on it. Erick, the regression tests, at least, should be succeeding now. Lincoln On Wed, Oct 7, 2009 at 9:21 AM, Scott Cain <scott@...> wrote: Hi Lincoln and Erick, -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) 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/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Getting a high-resolution image and its PDF in GBrowse 2
by Erick Antezana-4
::
Rate this Message:
Hi Lincoln, Scott,
indeed, there are no more errors reported while running the regression tests but two "harmless" warnings: t/01yeast.t ............... ok t/02.rearchitecture.t ..... ok t/03.render.t ............. 21/148 invalid track Motif at .../Generic-Genome-Browser/t/../lib/Bio/Graphics/Browser2/Render.pm line 1751. invalid track Motif at ...Generic-Genome-Browser/t/../lib/Bio/Graphics/Browser2/Render.pm line 1751. t/03.render.t ............. ok t/04.remoteserver.t ....... ok t/05.deferredrendering.t .. ok t/06.featuresearch.t ...... 24/25 Use of inherited AUTOLOAD for non-method DBI::DESTROY() is deprecated at /usr/local/lib/perl5/5.10.0/AutoLoader.pm line 51 during global destruction. t/06.featuresearch.t ...... ok t/07.karyotype.t .......... ok t/08.calign.t ............. ok All tests successful. Files=8, Tests=341, 16 wallclock secs ( 0.04 usr 0.04 sys + 3.38 cusr 0.47 csys = 3.93 CPU) Result: PASS cheers, Erick 2009/10/7 Lincoln Stein <lincoln.stein@...>: > Hi Scott, > > Thanks so much for finding these things. I'll work on it. > > Erick, the regression tests, at least, should be succeeding now. > > Lincoln > > On Wed, Oct 7, 2009 at 9:21 AM, Scott Cain <scott@...> wrote: >> >> Hi Lincoln and Erick, >> >> Based on a recursive grep through the source looking for "Browser" but >> not "Browser2", it looks to me like the following files may still need >> some fixing for the Browser->Browser2 change: >> >> Build.PL: copy("./libalign/$_" => "./lib/Bio/Graphics/Browser/$_"); >> bin/gbrowse_clean.pl:use Bio::Graphics::Browser; >> bin/gbrowse_slave:use Bio::Graphics::Browser::Render::Slave; >> cgi-bin/gbrowse_details:use Bio::Graphics::Browser; >> cgi-bin/gbrowse_gmap:use Bio::Graphics::Browser; >> cgi-bin/gbrowse_login:use Bio::Graphics::Browser; >> conf/plugins/PrimerDesigner.pm:use Bio::Graphics::Browser; >> contrib/Coverage/plugin/Coverage.pm:use Bio::Graphics::Browser::Plugin; >> contrib/TextDumper/TextDumper.pm:use Bio::Graphics::Browser::Plugin; >> libalign/CAlign.pm:package Bio::Graphics::Browser::CAlign; >> >> libalign/CAlign.xs:_do_alignment(packname="Bio::Graphics::Browser::CAlign",src,tgt,options=NULL) >> >> >> Scott >> >> >> On Wed, Oct 7, 2009 at 10:03 AM, Erick Antezana >> <erick.antezana@...> wrote: >> > Hi Lincoln, >> > >> > I have just SVN-updated my GBrowse 2 install. The high-res image >> > generations works fine. However, the PDF generation is still broken >> > :-( Could you please take a look at it? >> > >> > On the other hand, we were wondering whether the 'High-res Image' >> > should actually display (generate) an image of the actual tracks >> > layout that are displayed? The GBrowse 2.0 interface (AJAX-based) >> > allows users to move tracks (which is very useful) and stack them into >> > various ways (change_track_order). Nevertheless, if we move any track >> > and then click on 'High-res Image', we get an image displaying the >> > initial layout and not the one resulting after making some moves :-( >> > Would that be possible to have? >> > >> > I have realised that the directory (modules) >> > ...../Bio/Graphics/Browser has been renamed to >> > ...../Bio/Graphics/Browser2 , is it still needed to cascade this >> > renaming in the plugin "Reporter.pm"? >> > >> > Finally, the regression test are still reporting the same failures >> > as reported recently. >> > >> > thanks again, >> > Erick >> > >> > 2009/10/6 Lincoln Stein <lincoln.stein@...>: >> >> Sorry about the regression test failures. This will be fixed sometime >> >> today. >> >> >> >> Lincoln >> >> >> >> On Tue, Oct 6, 2009 at 5:03 AM, Erick Antezana >> >> <erick.antezana@...> >> >> wrote: >> >>> >> >>> Hi Lincoln, >> >>> >> >>> I have just SVN-updated my GBrowse install. After launching the >> >>> command >> >>> "Build test", I got a few warning and error messages: >> >>> >> >>> >> >>> t/02.rearchitecture.t ..... 1/90 Use of uninitialized value $dbid in >> >>> hash >> >>> element at >> >>> >> >>> /home/user/Generic-Genome-Browser/t/../lib/Bio/Graphics/Browser2/DataSource.pm >> >>> line 530. >> >>> >> >>> .... >> >>> >> >>> Can't locate object method "add_user_type" via package >> >>> "Bio::Graphics::Browser2::DataSource" at t/02.rearchitecture.t line >> >>> 263. >> >>> t/02.rearchitecture.t ..... Dubious, test returned 255 (wstat 65280, >> >>> 0xff00) >> >>> >> >>> >> >>> .... >> >>> >> >>> t/03.render.t ............. 123/148 Can't locate object method >> >>> "delete_track" via package "Bio::Graphics::Browser2::UserTracks" at >> >>> t/03.render.t line 496. >> >>> t/03.render.t ............. Dubious, test returned 255 (wstat 65280, >> >>> 0xff00) >> >>> >> >>> >> >>> I will come back to you later with the result of the tests regarding >> >>> th >> >>> high-res image generation. >> >>> >> >>> thanks, >> >>> Erick >> >>> >> >>> 2009/10/5 Lincoln Stein <lincoln.stein@...> >> >>>> >> >>>> Hi Erick, >> >>>> >> >>>> Could you do an SVN update to pick up the fix? If you are not >> >>>> comfortable >> >>>> with that I'll release a new version to CPAN tomorrow. >> >>>> >> >>>> Lincoln >> >>>> >> >>>> On Mon, Oct 5, 2009 at 2:54 PM, Erick Antezana >> >>>> <erick.antezana@...> >> >>>> wrote: >> >>>>> >> >>>>> Lincoln, >> >>>>> >> >>>>> it is happening in GBrowse 2.0 >> >>>>> >> >>>>> thanks, >> >>>>> Erick >> >>>>> >> >>>>> 2009/10/5 Lincoln Stein <lincoln.stein@...> >> >>>>>> >> >>>>>> Erick, is this happening in GBrowse 1.7 or 2.0? >> >>>>>> >> >>>>>> Lincoln >> >>>>>> >> >>>>>> On Mon, Oct 5, 2009 at 9:37 AM, Erick Antezana >> >>>>>> <erick.antezana@...> wrote: >> >>>>>>> >> >>>>>>> Hello, >> >>>>>>> >> >>>>>>> I have just updated my Bioperl install (live version). I tried >> >>>>>>> to >> >>>>>>> test the generation of a high-resolution image (by clicking on the >> >>>>>>> link >> >>>>>>> found in the header of the browser) and I got the following Apache >> >>>>>>> error >> >>>>>>> message (see full error log messages at the end of this email): >> >>>>>>> >> >>>>>>> Can't locate object method "create_cookie" via package >> >>>>>>> "Bio::Graphics::Browser::Render" at ...../cgi-bin/gbrowse_img line >> >>>>>>> 112. >> >>>>>>> >> >>>>>>> There seems to be a non-implemented subroutine? >> >>>>>>> >> >>>>>>> Some more info: >> >>>>>>> >> >>>>>>> GD version: 2.44 >> >>>>>>> GD::SVG version 0.33 >> >>>>>>> libgd version 2.0.33 >> >>>>>>> >> >>>>>>> >> >>>>>>> On the other hand, I have also tried to get an image in PDF >> >>>>>>> ([Download >> >>>>>>> PDF] link) and I got the same error message as above (see full log >> >>>>>>> at the >> >>>>>>> end of this email) but with some more details about some >> >>>>>>> non-implemented-yet >> >>>>>>> subroutines (e.g. clip, saveAlpha, alphaBlending). >> >>>>>>> >> >>>>>>> Any suggestions? >> >>>>>>> Erick >> >>>>>>> >> >>>>>>> p.s.1. Error log while trying to retrieve a high-res image >> >>>>>>> >> >>>>>>> [error] Useless use of a constant in void context at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 469, <DATA> line 192., referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] [14433] RUN(): GET: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> make_image=GD%3A%3ASVG at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 147., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] event(make_image) at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 266., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] Use of uninitialized value $mime_type in concatenation >> >>>>>>> (.) or >> >>>>>>> string at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] [14433] asynchronous event returning status=302, >> >>>>>>> mime-type= >> >>>>>>> at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] [14433] asynchronous exit at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 162., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] Useless use of a constant in void context at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 469, <DATA> line 192., referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] init() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 209., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] set_default_state() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 210., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] init_database() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 212., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] init_plugins() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 214., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] init_remote_sources() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 216., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] initializing uploaded files... at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >> >>>>>>> line 20., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] add_files_from_state() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >> >>>>>>> line 35., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] name_file() returns => >> >>>>>>> (file:foo,/data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo) >> >>>>>>> at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UserData.pm >> >>>>>>> line 127., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] @@@ /data/tmp/tmp_apache/userdata/yeast/uploads/erick/, >> >>>>>>> referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] init done at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 218., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] [14434] update_state() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 1909., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] [14434] CGI updated at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 1916., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] [14434] update_state() done at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 1932., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] FEATURESET = >> >>>>>>> Bio::Graphics::Browser::PluginSet=HASH(0x45a9a90), sources = at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] FEATURESET = >> >>>>>>> Bio::Graphics::Browser::UploadSet=HASH(0x500ac00), sources = at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] FEATURESET = >> >>>>>>> Bio::Graphics::Browser::RemoteSet=HASH(0x500ac48), sources = at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] FEATURE files = at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 3502., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] Can't locate object method "create_cookie" via package >> >>>>>>> "Bio::Graphics::Browser::Render" at >> >>>>>>> >> >>>>>>> /tools/bioinfo/apache/cgi-bin/Tools/GeneticAndGenomic/GGB/gbrowse_img line >> >>>>>>> 112., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] Premature end of script headers: gbrowse_img, referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> p.s.2. Error log while asking for an image in PDF format: >> >>>>>>> >> >>>>>>> [error] Useless use of a constant in void context at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 469, <DATA> line 192., referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] [14736] RUN(): GET: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> make_image=PDF at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 147., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] event(make_image) at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 266., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] Use of uninitialized value $mime_type in concatenation >> >>>>>>> (.) or >> >>>>>>> string at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] [14736] asynchronous event returning status=302, >> >>>>>>> mime-type= >> >>>>>>> at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] [14736] asynchronous exit at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 162., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] Useless use of a constant in void context at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 469, <DATA> line 192., referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] init() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 209., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] set_default_state() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 210., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] init_database() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 212., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] init_plugins() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 214., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] init_remote_sources() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 216., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] initializing uploaded files... at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >> >>>>>>> line 20., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] add_files_from_state() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >> >>>>>>> line 35., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] /data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo, >> >>>>>>> referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] name_file() returns => >> >>>>>>> (file:foo,/data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo) >> >>>>>>> at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UserData.pm >> >>>>>>> line 127., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] @@@ /data/tmp/tmp_apache/userdata/yeast/uploads/erick/, >> >>>>>>> referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] init done at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 218., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] [14737] update_state() at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 1909., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] [14737] CGI updated at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 1916., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] [14737] update_state() done at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 1932., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] FEATURESET = >> >>>>>>> Bio::Graphics::Browser::PluginSet=HASH(0x1e655d60), sources = at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] FEATURESET = >> >>>>>>> Bio::Graphics::Browser::UploadSet=HASH(0x1f0adc30), sources = at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] FEATURESET = >> >>>>>>> Bio::Graphics::Browser::RemoteSet=HASH(0x1f0adc78), sources = at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] FEATURE files = at >> >>>>>>> >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >> >>>>>>> line 3502., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method fill is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method fill is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method fill is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method fill is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method fill is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] GD method clip is not implemented in GD::SVG at >> >>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., >> >>>>>>> referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] Can't locate object method "create_cookie" via package >> >>>>>>> "Bio::Graphics::Browser::Render" at >> >>>>>>> >> >>>>>>> /tools/bioinfo/apache/cgi-bin/Tools/GeneticAndGenomic/GGB/gbrowse_img line >> >>>>>>> 112., referer: http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> [error] Premature end of script headers: gbrowse_img, referer: >> >>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> ------------------------------------------------------------------------------ >> >>>>>>> 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 >> >>>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> -- >> >>>>>> Lincoln D. Stein >> >>>>>> Director, Informatics and Biocomputing Platform >> >>>>>> Ontario Institute for Cancer Research >> >>>>>> 101 College St., Suite 800 >> >>>>>> Toronto, ON, Canada M5G0A3 >> >>>>>> 416 673-8514 >> >>>>>> Assistant: Renata Musa <Renata.Musa@...> >> >>>>> >> >>>> >> >>>> >> >>>> >> >>>> -- >> >>>> Lincoln D. Stein >> >>>> Director, Informatics and Biocomputing Platform >> >>>> Ontario Institute for Cancer Research >> >>>> 101 College St., Suite 800 >> >>>> Toronto, ON, Canada M5G0A3 >> >>>> 416 673-8514 >> >>>> Assistant: Renata Musa <Renata.Musa@...> >> >>> >> >> >> >> >> >> >> >> -- >> >> Lincoln D. Stein >> >> Director, Informatics and Biocomputing Platform >> >> Ontario Institute for Cancer Research >> >> 101 College St., Suite 800 >> >> Toronto, ON, Canada M5G0A3 >> >> 416 673-8514 >> >> Assistant: Renata Musa <Renata.Musa@...> >> >> >> > >> > >> > ------------------------------------------------------------------------------ >> > Come build with us! The BlackBerry(R) 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/devconference >> > _______________________________________________ >> > 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 > > > > -- > Lincoln D. Stein > Director, Informatics and Biocomputing Platform > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa <Renata.Musa@...> > ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) 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/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Getting a high-resolution image and its PDF in GBrowse 2
by Erick Antezana-4
::
Rate this Message:
Hi Lincoln,
I have just SVN-updated my local copy of GBrowse 2.x. Please find below some issues I found: 1. Renaming: Browser --> Browser2 /usr/local/bin/gbrowse_slave (4 ocurrences) /usr/local/bin/gbrowse_details (1 occ) /usr/local/bin/gbrowse_clean.pl (2 occ) 2. Some missing files after installing GBrowse 2.x (it works fine after copying them manually): tabs.js dropdown/: default_theme.css dropdown.css helper.css images dropdown/images: favicon.ico icon.png nav-arrow-down-on.png nav-arrow-down-open.png nav-arrow-down.png nav-arrow-left-on.png nav-arrow-left-open.png nav-arrow-left.png nav-arrow-right-on.png nav-arrow-right-open.png nav-arrow-right.png nav-arrow-up-on.png nav-arrow-up-open.png nav-arrow-up.png pattern1.png pattern2.png pattern3.png I have tested the 'tabbed menu', it works fine in Firefox, safari and IE 7. Unfortunately, it does not work under IE 6. cheers, Erick 2009/10/7 Scott Cain <scott@...>: > Hi Lincoln and Erick, > > Based on a recursive grep through the source looking for "Browser" but > not "Browser2", it looks to me like the following files may still need > some fixing for the Browser->Browser2 change: > > Build.PL: copy("./libalign/$_" => "./lib/Bio/Graphics/Browser/$_"); > bin/gbrowse_clean.pl:use Bio::Graphics::Browser; > bin/gbrowse_slave:use Bio::Graphics::Browser::Render::Slave; > cgi-bin/gbrowse_details:use Bio::Graphics::Browser; > cgi-bin/gbrowse_gmap:use Bio::Graphics::Browser; > cgi-bin/gbrowse_login:use Bio::Graphics::Browser; > conf/plugins/PrimerDesigner.pm:use Bio::Graphics::Browser; > contrib/Coverage/plugin/Coverage.pm:use Bio::Graphics::Browser::Plugin; > contrib/TextDumper/TextDumper.pm:use Bio::Graphics::Browser::Plugin; > libalign/CAlign.pm:package Bio::Graphics::Browser::CAlign; > libalign/CAlign.xs:_do_alignment(packname="Bio::Graphics::Browser::CAlign",src,tgt,options=NULL) > > > Scott > > > On Wed, Oct 7, 2009 at 10:03 AM, Erick Antezana > <erick.antezana@...> wrote: >> Hi Lincoln, >> >> I have just SVN-updated my GBrowse 2 install. The high-res image >> generations works fine. However, the PDF generation is still broken >> :-( Could you please take a look at it? >> >> On the other hand, we were wondering whether the 'High-res Image' >> should actually display (generate) an image of the actual tracks >> layout that are displayed? The GBrowse 2.0 interface (AJAX-based) >> allows users to move tracks (which is very useful) and stack them into >> various ways (change_track_order). Nevertheless, if we move any track >> and then click on 'High-res Image', we get an image displaying the >> initial layout and not the one resulting after making some moves :-( >> Would that be possible to have? >> >> I have realised that the directory (modules) >> ...../Bio/Graphics/Browser has been renamed to >> ...../Bio/Graphics/Browser2 , is it still needed to cascade this >> renaming in the plugin "Reporter.pm"? >> >> Finally, the regression test are still reporting the same failures >> as reported recently. >> >> thanks again, >> Erick >> >> 2009/10/6 Lincoln Stein <lincoln.stein@...>: >>> Sorry about the regression test failures. This will be fixed sometime today. >>> >>> Lincoln >>> >>> On Tue, Oct 6, 2009 at 5:03 AM, Erick Antezana <erick.antezana@...> >>> wrote: >>>> >>>> Hi Lincoln, >>>> >>>> I have just SVN-updated my GBrowse install. After launching the command >>>> "Build test", I got a few warning and error messages: >>>> >>>> >>>> t/02.rearchitecture.t ..... 1/90 Use of uninitialized value $dbid in hash >>>> element at >>>> /home/user/Generic-Genome-Browser/t/../lib/Bio/Graphics/Browser2/DataSource.pm >>>> line 530. >>>> >>>> .... >>>> >>>> Can't locate object method "add_user_type" via package >>>> "Bio::Graphics::Browser2::DataSource" at t/02.rearchitecture.t line 263. >>>> t/02.rearchitecture.t ..... Dubious, test returned 255 (wstat 65280, >>>> 0xff00) >>>> >>>> >>>> .... >>>> >>>> t/03.render.t ............. 123/148 Can't locate object method >>>> "delete_track" via package "Bio::Graphics::Browser2::UserTracks" at >>>> t/03.render.t line 496. >>>> t/03.render.t ............. Dubious, test returned 255 (wstat 65280, >>>> 0xff00) >>>> >>>> >>>> I will come back to you later with the result of the tests regarding th >>>> high-res image generation. >>>> >>>> thanks, >>>> Erick >>>> >>>> 2009/10/5 Lincoln Stein <lincoln.stein@...> >>>>> >>>>> Hi Erick, >>>>> >>>>> Could you do an SVN update to pick up the fix? If you are not comfortable >>>>> with that I'll release a new version to CPAN tomorrow. >>>>> >>>>> Lincoln >>>>> >>>>> On Mon, Oct 5, 2009 at 2:54 PM, Erick Antezana <erick.antezana@...> >>>>> wrote: >>>>>> >>>>>> Lincoln, >>>>>> >>>>>> it is happening in GBrowse 2.0 >>>>>> >>>>>> thanks, >>>>>> Erick >>>>>> >>>>>> 2009/10/5 Lincoln Stein <lincoln.stein@...> >>>>>>> >>>>>>> Erick, is this happening in GBrowse 1.7 or 2.0? >>>>>>> >>>>>>> Lincoln >>>>>>> >>>>>>> On Mon, Oct 5, 2009 at 9:37 AM, Erick Antezana >>>>>>> <erick.antezana@...> wrote: >>>>>>>> >>>>>>>> Hello, >>>>>>>> >>>>>>>> I have just updated my Bioperl install (live version). I tried to >>>>>>>> test the generation of a high-resolution image (by clicking on the link >>>>>>>> found in the header of the browser) and I got the following Apache error >>>>>>>> message (see full error log messages at the end of this email): >>>>>>>> >>>>>>>> Can't locate object method "create_cookie" via package >>>>>>>> "Bio::Graphics::Browser::Render" at ...../cgi-bin/gbrowse_img line 112. >>>>>>>> >>>>>>>> There seems to be a non-implemented subroutine? >>>>>>>> >>>>>>>> Some more info: >>>>>>>> >>>>>>>> GD version: 2.44 >>>>>>>> GD::SVG version 0.33 >>>>>>>> libgd version 2.0.33 >>>>>>>> >>>>>>>> >>>>>>>> On the other hand, I have also tried to get an image in PDF ([Download >>>>>>>> PDF] link) and I got the same error message as above (see full log at the >>>>>>>> end of this email) but with some more details about some non-implemented-yet >>>>>>>> subroutines (e.g. clip, saveAlpha, alphaBlending). >>>>>>>> >>>>>>>> Any suggestions? >>>>>>>> Erick >>>>>>>> >>>>>>>> p.s.1. Error log while trying to retrieve a high-res image >>>>>>>> >>>>>>>> [error] Useless use of a constant in void context at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] [14433] RUN(): GET: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> make_image=GD%3A%3ASVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 147., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] event(make_image) at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 266., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] Use of uninitialized value $mime_type in concatenation (.) or >>>>>>>> string at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] [14433] asynchronous event returning status=302, mime-type= >>>>>>>> at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] [14433] asynchronous exit at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 162., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] Useless use of a constant in void context at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] init() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 209., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] set_default_state() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 210., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] init_database() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 212., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] init_plugins() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 214., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] init_remote_sources() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 216., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] initializing uploaded files... at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >>>>>>>> line 20., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] add_files_from_state() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >>>>>>>> line 35., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] name_file() returns => >>>>>>>> (file:foo,/data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo) at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UserData.pm >>>>>>>> line 127., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] @@@ /data/tmp/tmp_apache/userdata/yeast/uploads/erick/, >>>>>>>> referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] init done at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 218., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] [14434] update_state() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 1909., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] [14434] CGI updated at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 1916., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] [14434] update_state() done at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 1932., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] FEATURESET = >>>>>>>> Bio::Graphics::Browser::PluginSet=HASH(0x45a9a90), sources = at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] FEATURESET = >>>>>>>> Bio::Graphics::Browser::UploadSet=HASH(0x500ac00), sources = at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] FEATURESET = >>>>>>>> Bio::Graphics::Browser::RemoteSet=HASH(0x500ac48), sources = at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] FEATURE files = at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 3502., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] Can't locate object method "create_cookie" via package >>>>>>>> "Bio::Graphics::Browser::Render" at >>>>>>>> /tools/bioinfo/apache/cgi-bin/Tools/GeneticAndGenomic/GGB/gbrowse_img line >>>>>>>> 112., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] Premature end of script headers: gbrowse_img, referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> p.s.2. Error log while asking for an image in PDF format: >>>>>>>> >>>>>>>> [error] Useless use of a constant in void context at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] [14736] RUN(): GET: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> make_image=PDF at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 147., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] event(make_image) at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 266., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] Use of uninitialized value $mime_type in concatenation (.) or >>>>>>>> string at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] [14736] asynchronous event returning status=302, mime-type= >>>>>>>> at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 227., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] [14736] asynchronous exit at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 162., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] Useless use of a constant in void context at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 469, <DATA> line 192., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] init() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 209., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] set_default_state() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 210., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] init_database() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 212., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] init_plugins() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 214., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] init_remote_sources() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 216., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] initializing uploaded files... at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >>>>>>>> line 20., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] add_files_from_state() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UploadSet.pm >>>>>>>> line 35., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] /data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo, >>>>>>>> referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] name_file() returns => >>>>>>>> (file:foo,/data/tmp/tmp_apache/userdata/yeast/uploads/erick/foo) at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/UserData.pm >>>>>>>> line 127., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] @@@ /data/tmp/tmp_apache/userdata/yeast/uploads/erick/, >>>>>>>> referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] init done at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 218., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] [14737] update_state() at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 1909., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] [14737] CGI updated at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 1916., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] [14737] update_state() done at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 1932., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] FEATURESET = >>>>>>>> Bio::Graphics::Browser::PluginSet=HASH(0x1e655d60), sources = at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] FEATURESET = >>>>>>>> Bio::Graphics::Browser::UploadSet=HASH(0x1f0adc30), sources = at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] FEATURESET = >>>>>>>> Bio::Graphics::Browser::RemoteSet=HASH(0x1f0adc78), sources = at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 3493., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] FEATURE files = at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Render.pm >>>>>>>> line 3502., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method saveAlpha is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method fill is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method alphaBlending is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] GD method clip is not implemented in GD::SVG at >>>>>>>> /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 196., referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] Can't locate object method "create_cookie" via package >>>>>>>> "Bio::Graphics::Browser::Render" at >>>>>>>> /tools/bioinfo/apache/cgi-bin/Tools/GeneticAndGenomic/GGB/gbrowse_img line >>>>>>>> 112., referer: http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> [error] Premature end of script headers: gbrowse_img, referer: >>>>>>>> http://erick/cgi-bin/gbrowse/yeast/ >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------------ >>>>>>>> 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 >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Lincoln D. Stein >>>>>>> Director, Informatics and Biocomputing Platform >>>>>>> Ontario Institute for Cancer Research >>>>>>> 101 College St., Suite 800 >>>>>>> Toronto, ON, Canada M5G0A3 >>>>>>> 416 673-8514 >>>>>>> Assistant: Renata Musa <Renata.Musa@...> >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Lincoln D. Stein >>>>> Director, Informatics and Biocomputing Platform >>>>> Ontario Institute for Cancer Research >>>>> 101 College St., Suite 800 >>>>> Toronto, ON, Canada M5G0A3 >>>>> 416 673-8514 >>>>> Assistant: Renata Musa <Renata.Musa@...> >>>> >>> >>> >>> >>> -- >>> Lincoln D. Stein >>> Director, Informatics and Biocomputing Platform >>> Ontario Institute for Cancer Research >>> 101 College St., Suite 800 >>> Toronto, ON, Canada M5G0A3 >>> 416 673-8514 >>> Assistant: Renata Musa <Renata.Musa@...> >>> >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry(R) 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/devconference >> _______________________________________________ >> 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(R) 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/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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