[Gmod-gbrowse] SVG & PNG export failed

[Thomas LETELLIER]

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

[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
/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.
[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
[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
[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