diff -Nru libbio-graphics-perl-2.40/debian/changelog libbio-graphics-perl-2.40/debian/changelog --- libbio-graphics-perl-2.40/debian/changelog 2018-09-21 20:50:17.000000000 +0000 +++ libbio-graphics-perl-2.40/debian/changelog 2019-11-25 13:48:39.000000000 +0000 @@ -1,3 +1,32 @@ +libbio-graphics-perl (2.40-6) unstable; urgency=medium + + * Team upload. + * Add dependency on libbio-db-seqfeature-perl + + -- Michael R. Crusoe Mon, 25 Nov 2019 14:48:39 +0100 + +libbio-graphics-perl (2.40-5) unstable; urgency=medium + + * Team upload. + * debian/control: Breaks+Replaces the old libbio-bio-perl. (Closes: #942789) + * debian/patches/spelling: fix typos + + -- Michael R. Crusoe Sat, 23 Nov 2019 09:23:09 +0100 + +libbio-graphics-perl (2.40-4) unstable; urgency=medium + + * Team upload. + * debhelper-compat 12 + * Standards-Version: 4.4.0 + * Secure URI in copyright format + * Remove trailing whitespace in debian/changelog + * Set fields Upstream-Name, Upstream-Contact in debian/copyright. + * Remove obsolete fields Name, Contact from debian/upstream/metadata. + * Add build-dep on libbio-db-seqfeature-perl which was split from bioperl + (Closes: #942063) + + -- Michael R. Crusoe Tue, 12 Nov 2019 14:05:45 +0100 + libbio-graphics-perl (2.40-3) unstable; urgency=medium * debhelper 11 @@ -28,7 +57,7 @@ * New upstream version * Build-Depends: libbio-coordinate-perl - Closes: #848105 + Closes: #848105 * debhelper 10 * d/watch: version=4 * d/control: Testsuite: autopkgtest-pkg-perl @@ -53,7 +82,7 @@ libbio-graphics-perl (2.39-3) unstable; urgency=medium - * Add libmodule-build-perl dep (Closes: #789063). + * Add libmodule-build-perl dep (Closes: #789063). -- Olivier Sallou Fri, 19 Jun 2015 11:19:26 +0200 diff -Nru libbio-graphics-perl-2.40/debian/compat libbio-graphics-perl-2.40/debian/compat --- libbio-graphics-perl-2.40/debian/compat 2018-09-21 20:50:17.000000000 +0000 +++ libbio-graphics-perl-2.40/debian/compat 1970-01-01 00:00:00.000000000 +0000 @@ -1 +0,0 @@ -11 diff -Nru libbio-graphics-perl-2.40/debian/control libbio-graphics-perl-2.40/debian/control --- libbio-graphics-perl-2.40/debian/control 2018-09-21 20:50:17.000000000 +0000 +++ libbio-graphics-perl-2.40/debian/control 2019-11-25 13:48:14.000000000 +0000 @@ -5,7 +5,7 @@ Section: perl Testsuite: autopkgtest-pkg-perl Priority: optional -Build-Depends: debhelper (>= 11~), +Build-Depends: debhelper-compat (= 12), libmodule-build-perl, perl # Needed for the tests @@ -13,10 +13,11 @@ libgd-perl, libstatistics-descriptive-perl, libgd-svg-perl, - libcgi-pm-perl | perl (<< 5.19), + libcgi-pm-perl, libbio-coordinate-perl, + libbio-db-seqfeature-perl, rename -Standards-Version: 4.2.1 +Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/libbio-graphics-perl Vcs-Git: https://salsa.debian.org/med-team/libbio-graphics-perl.git Homepage: https://metacpan.org/release/Bio-Graphics @@ -26,7 +27,10 @@ Depends: ${perl:Depends}, ${misc:Depends}, bioperl, - libgd-gd2-perl + libgd-gd2-perl, + libbio-db-seqfeature-perl +Breaks: libbio-perl-perl (<< 1.7.3) +Replaces: libbio-perl-perl (<< 1.7.3) Recommends: libbio-scf-perl, perl, libberkeleydb-perl, diff -Nru libbio-graphics-perl-2.40/debian/copyright libbio-graphics-perl-2.40/debian/copyright --- libbio-graphics-perl-2.40/debian/copyright 2018-09-21 20:50:17.000000000 +0000 +++ libbio-graphics-perl-2.40/debian/copyright 2019-11-23 08:23:09.000000000 +0000 @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/Bio-Graphics-2.40.tar.gz Comment: On Debian systems, copies of the GNU General Public License version 1 and Lesser General Public License version 2.1 can be found respectively in @@ -7,6 +7,8 @@ Most files in this package are distributed under the same terms as Perl itself, but there are also a few files under ‘LGPL-2.1+ or Artistic-2.0’ or ‘GPL-1+ or Artistic-2.0’, which are compatible. +Upstream-Name: Bio::Graphics +Upstream-Contact: Lincoln Stein Files: * Copyright: 2001-2010, Cold Spring Harbor Laboratory @@ -190,4 +192,3 @@ found in ‘/usr/share/common-licenses/Artistic’, and the complete text of the latest version of the GNU General Public License version 1 can be found in ‘/usr/share/common-licenses/GPL-1’. - diff -Nru libbio-graphics-perl-2.40/debian/patches/series libbio-graphics-perl-2.40/debian/patches/series --- libbio-graphics-perl-2.40/debian/patches/series 2018-09-21 20:50:17.000000000 +0000 +++ libbio-graphics-perl-2.40/debian/patches/series 2019-11-23 08:33:22.000000000 +0000 @@ -1 +1,2 @@ unescaped_left_brace.patch +spelling diff -Nru libbio-graphics-perl-2.40/debian/patches/spelling libbio-graphics-perl-2.40/debian/patches/spelling --- libbio-graphics-perl-2.40/debian/patches/spelling 1970-01-01 00:00:00.000000000 +0000 +++ libbio-graphics-perl-2.40/debian/patches/spelling 2019-11-23 08:35:06.000000000 +0000 @@ -0,0 +1,148 @@ +From: Michael R. Crusoe +Subject: Fix a few typos +--- libbio-graphics-perl.orig/lib/Bio/Graphics/Feature.pm ++++ libbio-graphics-perl/lib/Bio/Graphics/Feature.pm +@@ -260,7 +260,7 @@ + called the accession_number. For sequences from established + databases, the implementors should try to use the correct + accession number. Notice that primary_id() provides the +- unique id for the implemetation, allowing multiple objects ++ unique id for the implementation, allowing multiple objects + to have the same accession number in a particular implementation. + + For sequences with no accession number, this method should return +--- libbio-graphics-perl.orig/lib/Bio/Graphics/FeatureFile.pm ++++ libbio-graphics-perl/lib/Bio/Graphics/FeatureFile.pm +@@ -314,7 +314,7 @@ + + -safe_world If the -safe option is not set, and -safe_world + is set to a true value, then Bio::Graphics::FeatureFile +- will evalute "sub {}" options in a L ++ will evaluate "sub {}" options in a L + environment with minimum permissions. Subroutines + will be able to access and interrogate + Bio::DB::SeqFeature objects and perform basic Perl +--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/decorated_transcript.pm ++++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/decorated_transcript.pm +@@ -17,7 +17,7 @@ + sub my_descripton { + return <get_tag_values(DECORATION_TAG_NAME); + } + +-# allows to retrieve additional decorations via callback ++# allows one to retrieve additional decorations via callback + sub additional_decorations { + my $self = shift; + my $feature = $self->feature; +@@ -948,7 +948,7 @@ + =head1 DESCRIPTION + + This glyph extends the functionality of the L glyph +-and allows to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains) ++and allows one to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains) + on top of gene models. Currently, the glyph can draw decorations in form of colored or outlined boxes + inside or around CDS segments. Protein decorations are specified at the 'mRNA' transcript level + in protein coordinates. Protein coordinates are automatically mapped to nucleotide coordinates by the glyph. +--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/fb_shmiggle.pm ++++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/fb_shmiggle.pm +@@ -611,7 +611,7 @@ +
+
+ +-Setting 'subsetsnames' allows to rename subsets (very important as in most cases ++Setting 'subsetsnames' allows one to rename subsets (very important as in most cases + workflow names of subsets are unsutable for intelligent data display to end users). + If setting omitted, initial subsets names will be used for display. + +--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/heat_map.pm ++++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/heat_map.pm +@@ -522,7 +522,7 @@ + white->red. + + For the start_color and end_color options, 140 named webcolors +-and their corresponsing RGB hex codes (listed below) are supported. ++and their corresponding RGB hex codes (listed below) are supported. + + steelblue #4682B4 + royalblue #041690 +--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/ideogram.pm ++++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/ideogram.pm +@@ -298,7 +298,7 @@ + $self->wipe(@_); + + # For single, unaggregated bands, make the terminal band +- # a bit wider to accomodate the arc ++ # a bit wider to accommodate the arc + if ($self->{single}) { + $x1 -= 5 if $state == 1; + $x2 += 5 if $state == 0; +--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/segments.pm ++++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/segments.pm +@@ -1136,7 +1136,7 @@ + hit() method, and both the source and the target DNA must be + available. If you pass the glyph a series of + Bio::SeqFeature::SimilarityPair objects, then these criteria will be +-satisified. ++satisfied. + + Without additional help, this glyph cannot display gapped alignments + correctly. To display gapped alignments, you can use the +--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/trace.pm ++++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/trace.pm +@@ -733,7 +733,7 @@ + installed). + + Until an alignment feature is added to this glyph, the feature start and end +-must correspond exactly with the begining and end of the called sequence. ++must correspond exactly with the beginning and end of the called sequence. + Meaning that even if the starting sequence is poor and doesn't match the + sequence, it must still be included. + +@@ -883,7 +883,7 @@ + + =head1 BUGS AND LIMITATIONS + +-See the L for an explaination of how to align the trace with the ++See the L for an explanation of how to align the trace with the + reference. + + The trace looks a little off when the feature is on the negative strand of the +--- libbio-graphics-perl.orig/lib/Bio/Graphics/Panel.pm ++++ libbio-graphics-perl/lib/Bio/Graphics/Panel.pm +@@ -1710,7 +1710,7 @@ + -auto_pad If "left" or "right" keys are in use true + then setting auto_pad to a true value + will allow the panel to adjust its +- width in order to accomodate the ++ width in order to accommodate the + length of the longest key. + + -empty_tracks What to do when a track is empty. suppress +@@ -1758,7 +1758,7 @@ + Useful when working with the + "image" glyph. + +- -truetype Render text using scaleable vector false ++ -truetype Render text using scalable vector false + fonts rather than bitmap fonts. + + -image_class To create output in scalable vector +--- libbio-graphics-perl.orig/lib/Bio/Graphics/Wiggle/Loader.pm ++++ libbio-graphics-perl/lib/Bio/Graphics/Wiggle/Loader.pm +@@ -101,7 +101,7 @@ + + =back + +-Example entended track declaration: ++Example intended track declaration: + + track type=wiggle_0 name="example" description="20 degrees, 2 hr" \ + trim=stdev2 transform=logsquared diff -Nru libbio-graphics-perl-2.40/debian/upstream/metadata libbio-graphics-perl-2.40/debian/upstream/metadata --- libbio-graphics-perl-2.40/debian/upstream/metadata 2018-09-21 20:50:17.000000000 +0000 +++ libbio-graphics-perl-2.40/debian/upstream/metadata 2019-11-12 13:00:15.000000000 +0000 @@ -1,3 +1 @@ Archive: CPAN -Contact: Lincoln Stein -Name: Bio::Graphics