From: Lincoln S. <lin...@gm...> - 2009-10-05 18:19:31
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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 <eri...@gm...>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 > Gmo...@li... > 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 <Ren...@oi...> |