Your message dated Wed, 18 Jan 2017 16:34:04 +0000 with message-id <[email protected]> and subject line Bug#848236: fixed in gbrowse 2.56+dfsg-1 has caused the Debian Bug report #848236, regarding src:gbrowse: Fails to build from source since bioperl upgrade has broken libbio-graphics-perl to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 848236: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=848236 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---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)
--- End Message ---
--- Begin Message ---Source: gbrowse Source-Version: 2.56+dfsg-1 We believe that the bug you reported is fixed in the latest version of gbrowse, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (supplier of updated gbrowse package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 18 Jan 2017 17:16:19 +0100 Source: gbrowse Binary: gbrowse gbrowse-data gbrowse-calign Architecture: source amd64 all Version: 2.56+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Tille <[email protected]> Description: gbrowse - GMOD Generic Genome Browser gbrowse-calign - CAlign helper gbrowse-data - Sample data to use GBrowse Closes: 826458 833885 848236 Changes: gbrowse (2.56+dfsg-1) unstable; urgency=medium . [ Olivier Sallou ] * Fix deprecated unescaped left brace in regex Closes: #826458 . [ Andreas Tille ] * New upstream version Closes: #848236 * Symlink OpenID constumer secret to /etc/gbrowse/ConfigData.pm and document this in README.Debian Closes: #833885 * debhelper 10 * d/watch: version=4 * Exclude some tests via debian/tests/pkg-perl/smoke-skip * Add missing Build-Depends: libbio-graphics-perl, libbio-coordinate-perl * Enhance descriptions * hardening=+all * Remove unused lintian override * Add $remote_fs to required-start * Add missing Depends: lsb-base (>= 3.0-6) * Fix runlevel of initscript * Fix manpage synopsises and spelling * Init lsb functions in all init scripts * Add missing "update-rc.d gbrowse-aws-balancer" calls Checksums-Sha1: 22501e2a43df3dacafaa3f948ef6d7054d3caf69 2641 gbrowse_2.56+dfsg-1.dsc 269fba6b75112b0a2037350308914f05d4747697 4355977 gbrowse_2.56+dfsg.orig.tar.gz 7e59e2a3845af9e05428c21295f5608dd14c8e83 22284 gbrowse_2.56+dfsg-1.debian.tar.xz 2a079697dfab0a1d8775cbd7ef300decb29250bd 27932 gbrowse-calign-dbgsym_2.56+dfsg-1_amd64.deb 62b246fb48e723e48c8b08f9ef1b890a8920a2e7 35794 gbrowse-calign_2.56+dfsg-1_amd64.deb 9b71506aacaff0080b4b367389f26fe3111c651b 1234536 gbrowse-data_2.56+dfsg-1_all.deb dd8457a4a82e6cd0eee47863aef51f6657dd67ed 2376460 gbrowse_2.56+dfsg-1_all.deb 3933e56299ffbea133aeb1636ec5e26cec8a3a33 8349 gbrowse_2.56+dfsg-1_amd64.buildinfo Checksums-Sha256: 248ff3221d27950baa8cebe5bdf5f27b941de0162d75f70e6ed9c8696f9f5136 2641 gbrowse_2.56+dfsg-1.dsc f6da1ff315b17ec260810cf439a54ae7ddd66728015be03f7fbb6ba795676f81 4355977 gbrowse_2.56+dfsg.orig.tar.gz 6bb109a315a8c998aea87b41b58247dc41f855a43f2faca0538851cb7a651b45 22284 gbrowse_2.56+dfsg-1.debian.tar.xz fc6949cb40e7b4b2cbb9d969feda0e285ac4f7f06c3ddad6560878cfde203f5e 27932 gbrowse-calign-dbgsym_2.56+dfsg-1_amd64.deb 8d4311b886643ff8f02e51514984f4e7fd467438830b94e3cee6e505f63311bd 35794 gbrowse-calign_2.56+dfsg-1_amd64.deb ad4fa399e6c9e271ccc3aa648f30908d0afbfc01f43925b264107d8b9254514d 1234536 gbrowse-data_2.56+dfsg-1_all.deb 0c35efefd08ef8f24c00dde5999354bd34f5ce1acf6b5873829e58bc7363fcaa 2376460 gbrowse_2.56+dfsg-1_all.deb a098fa0ef76022ab49afc43ba5159d3b3036c265eec685816d1be4b1ef76d421 8349 gbrowse_2.56+dfsg-1_amd64.buildinfo Files: 389aa71b47fccb7a51069d4655a5bf5c 2641 science optional gbrowse_2.56+dfsg-1.dsc 9638dd3e43897548172911706277f177 4355977 science optional gbrowse_2.56+dfsg.orig.tar.gz 66459ba99292df4f861f9e0354bfa9d6 22284 science optional gbrowse_2.56+dfsg-1.debian.tar.xz 9a13b1a1c180467561c7cdfb65c81eda 27932 debug extra gbrowse-calign-dbgsym_2.56+dfsg-1_amd64.deb 119584e9543decac6e5b202c6edeaf64 35794 science optional gbrowse-calign_2.56+dfsg-1_amd64.deb bbb037cda01422da94524072774b4bf1 1234536 science optional gbrowse-data_2.56+dfsg-1_all.deb 821faded43382c17c3ea79a179a71967 2376460 science optional gbrowse_2.56+dfsg-1_all.deb f2082fd5e24a4dc80737a6ed31e33edf 8349 science optional gbrowse_2.56+dfsg-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJYf5YSAAoJEFeKBJTRxkbRA2EP/3h6IqKnUMK7lsRcQNHjPLxX FLUbJzjIV/AN+WnooRS69m/Vg8F4MRIRVdaaZCcXeH4qxp7FkMxtFbCiNpsGAgSF DNKOyMfdcSn2zEmR53tQu7sgjZMrGfA4JN/TYiOIT0ZMXwmgHRpYC3mZaVzmJcEh PMzcam4X+hSljNNRuYujg2y69K509DFJnVR032PgoxDhCgdGrv5LwzvgcebXZyJZ BCiM0xij+/+gY0DzeqHHrlVvu22WWTsVYgVPuRN7LlwiaYxawpftZijeuUN6/5Iy Rsvl8SWeFRq67jRqkxxNFDUb2KYeaALYAEokctYYx/Y1DC/44WC3XYSKLkRu/VdP xvp4b740JzvBcO/392WB3ZpGGAbLnIz+xLvKxKY/TngPhVK50+reSRN6qrjII8Ep BY4XRJrmGYpEGvOqXarSTt1jtGtq/93OkgJjhLBAXrF43YD2lHjnVFWBVI2kDT1H CsfNcxO6T3d3XAAHWSatQg8UbdBrWBqcFWZNnriX1n3fkEsgIDCfbesCfU6WvZNV PDNP2MdBfr8rQxE0pnuKGrnC9u+P4cfLPC//jRS5gKOenewAxehHeDRRbaSpSZxN 6oBbBXiMrHXEfIe0CteMiBd1929JBcBQPiEWMaZlneH9uJdA6yMbRtlmh2PLi0Uw ugkl1En60wzGO8FO1jJO =hkWu -----END PGP SIGNATURE-----
--- End Message ---
