Package: src:gbrowse Severity: serious Justification: FTBFS Hi,
when trying to build gbrowse it fails to build from source: ... CGI::param called in list context from /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render.pm line 2348, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 412. CGI::param called in list context from /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 271, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 412, <STDIN> line 1. CGI::param called in list context from /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 271, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 412, <STDIN> line 1. RenderPanels error: ------------- EXCEPTION ------------- MSG: The requested glyph class, ``span'' is not available: Attempt to reload Bio/Graphics/Glyph/span.pm aborted. Compilation failed in require at (eval 180) line 2, <> line 45. STACK Bio::Graphics::Glyph::Factory::make_glyph /usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342 STACK Bio::Graphics::Glyph::add_feature /usr/share/perl5/Bio/Graphics/Glyph.pm:424 STACK Bio::Graphics::Browser2::RenderPanels::add_features_to_track /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1842 STACK (eval) /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1570 STACK Bio::Graphics::Browser2::RenderPanels::run_local_requests /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1524 STACK Bio::Graphics::Browser2::RenderPanels::request_panels /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:195 STACK Bio::Graphics::Browser2::Render::render_deferred /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render.pm:3589 STACK toplevel t/05.deferredrendering.t:102 ------------------------------------- ... The cause is most probably that libbio-graphics-perl does not work together with bioperl 1.7.1 (see also #848105). I'm now becoming aware that with the naive upgrade to bioperl 1.7.1 we have triggered problems that should have solved inside a transition via experimental. My proposed course of action is as follows: 1. Revert the version bump of bioperl and upload the old version with an epoch (1:1.6.924-6). 2. Upload 1.7.1-2 to experimental 3. Solve all issues with BioPerl 1.7.x after Stretch release. Does anybody have a better plan? Kind regards Andreas. -- System Information: Debian Release: 8.6 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system)