Re: [Gmod-gbrowse] Getting a high-resolution image and its PDF in GBrowse 2

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Lincoln,

 it is happening in GBrowse 2.0

thanks,
Erick

2009/10/5 Lincoln Stein <lin...@gm...>

> Erick, is this happening in GBrowse 1.7 or 2.0?
>
> 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/
>>
>>
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>
>
> --
> 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...>
>