SVG & PNG export failed

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SVG & PNG export failed

Thomas LETELLIER-2
Hello,

I have a trouble with images export with my GBrowse, I saw in the
documentation that it was a known bug, but I did not find any solution
to this problem...

When I click on the export I get an "Internal server error" with this
stack :

> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] Can't locate
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> \t/home/gbrowse/webapps/GBrowse-2.33/etc/gbrowse2/plugins/GFFDumper.pm
> in @INC (@INC contains:
> /home/gbrowse/webapps/GBrowse-2.33/etc/gbrowse2/plugins
> /usr/local/lib64/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5
> /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl
> /usr/lib64/perl5 /usr/share/perl5 .) at
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/PluginSet.pm line 31 (#1)
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] (F) You
> said to do (or require, or use) a file that couldn't be
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] found.
> Perl looks for the file in all the locations mentioned in @INC,
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] unless the
> file name included the full path to the file.  Perhaps you
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] need to
> set the PERL5LIB or PERL5OPT environment variable to say where
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] the extra
> library is, or maybe the script needs to add the library name
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]     to
> @INC.  Or maybe you just misspelled the name of the file.  See
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> perlfunc/require and lib.
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] Can't call
> method "seq_id" on an undefined value at
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> \t/usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line
> 1971 (#2)
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] (F) You
> used the syntax of a method call, but the slot filled by the
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] object
> reference or package name contains an undefined value. Something
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] like this
> will reproduce the error:
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]        
> $BADREF = undef;
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]        
> process $BADREF 1,2,3;
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]        
> $BADREF->process(1,2,3);
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] Uncaught
> exception from user code:
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] \tCan't
> call method "seq_id" on an undefined value at
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 1971.
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]  at
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 1971.
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> \tBio::Graphics::Browser2::RenderPanels::create_panel_args(Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0),
> HASH(0x56fb120)) called at
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 259
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> \tBio::Graphics::Browser2::RenderPanels::make_requests(Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0),
> HASH(0x56fb120)) called at
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 130
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> \tBio::Graphics::Browser2::RenderPanels::request_panels(Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0),
> HASH(0x56fb120)) called at
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 219
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> \tBio::Graphics::Browser2::RenderPanels::render_track_images(Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0),
> HASH(0x56fb120)) called at
> /home/gbrowse/webapps/GBrowse-2.33/var/www/cgi-bin/gb2/gbrowse_img
> line 311
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> \tGBrowse_img::render_tracks(GBrowse_img=HASH(0x4e32de0),
> Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0), "GD", 0, undef)
> called at
> /home/gbrowse/webapps/GBrowse-2.33/var/www/cgi-bin/gb2/gbrowse_img
> line 217
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> \tGBrowse_img::render_image(GBrowse_img=HASH(0x4e32de0)) called at
> /home/gbrowse/webapps/GBrowse-2.33/var/www/cgi-bin/gb2/gbrowse_img
> line 139
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> \tGBrowse_img::run(GBrowse_img=HASH(0x4e32de0)) called at
> /home/gbrowse/webapps/GBrowse-2.33/var/www/cgi-bin/gb2/gbrowse_img line 73
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] Premature
> end of script headers: gbrowse_img


My GBrowse version is 2.33 and I saw that GFFDumper.pm was deprecated
since 2.0, so the error message does not helped me a lot...

Best regards,

Thomas





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