[med-svn] [Git][med-team/libbio-graphics-perl][master] 3 commits: Breaks+Replaces the old libbio-bio-perl
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Nov 23 08:38:01 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / libbio-graphics-perl
Commits:
e55f0bc5 by Michael R. Crusoe at 2019-11-23T08:22:30Z
Breaks+Replaces the old libbio-bio-perl
- - - - -
f151b2f9 by Michael R. Crusoe at 2019-11-23T08:35:06Z
spelling
- - - - -
5a52c218 by Michael R. Crusoe at 2019-11-23T08:35:06Z
release to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/spelling
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+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 <michael.crusoe at gmail.com> Sat, 23 Nov 2019 09:23:09 +0100
+
libbio-graphics-perl (2.40-4) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -28,6 +28,8 @@ Depends: ${perl:Depends},
${misc:Depends},
bioperl,
libgd-gd2-perl
+Breaks: libbio-perl-perl (<< 1.7.3)
+Replaces: libbio-perl-perl (<< 1.7.3)
Recommends: libbio-scf-perl,
perl,
libberkeleydb-perl,
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
unescaped_left_brace.patch
+spelling
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,148 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+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<Safe::World>
++ will evaluate "sub {}" options in a L<Safe::World>
+ 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 <<END;
+ This glyph extends the functionality of the Bio::Graphics::Glyph::processed_transcript 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.
+@@ -201,7 +201,7 @@
+ return $feature->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<Bio::Graphics::Glyph::processed_transcript> 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 @@
+ <br>
+ <br>
+
+-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<DESCRIPTION> for an explaination of how to align the trace with the
++See the L<DESCRIPTION> 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
View it on GitLab: https://salsa.debian.org/med-team/libbio-graphics-perl/compare/7d7fce384d211e08e6d3967e4325c5e459740f53...5a52c2185812eab280977b96dcc7a13d9de67534
--
View it on GitLab: https://salsa.debian.org/med-team/libbio-graphics-perl/compare/7d7fce384d211e08e6d3967e4325c5e459740f53...5a52c2185812eab280977b96dcc7a13d9de67534
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