[med-svn] [Git][med-team/libbio-cluster-perl][master] 2 commits: routine-update: Ready to upload to unstable
Michael R. Crusoe
gitlab at salsa.debian.org
Tue Jan 7 13:35:02 GMT 2020
Michael R. Crusoe pushed to branch master at Debian Med / libbio-cluster-perl
Commits:
723a340a by Michael R. Crusoe at 2020-01-07T14:25:00+01:00
routine-update: Ready to upload to unstable
- - - - -
056967c7 by Michael R. Crusoe at 2020-01-07T14:34:29+01:00
use libbio-variation-perl
- - - - -
4 changed files:
- debian/changelog
- debian/control
- − debian/patches/delete-bio-variation-parts
- − debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,16 @@
+libbio-cluster-perl (1.7.3-4) unstable; urgency=medium
+
+ * libbio-variation-perl is in the archive, so remove our patch that avoided
+ it.
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Tue, 07 Jan 2020 14:34:20 +0100
+
libbio-cluster-perl (1.7.3-3) unstable; urgency=medium
* Whoops, try that again:
Strengthen Breaks+Replaces: libbio-perl-perl (<< 1.7.3) (Closes: #946568)
- -- Michael R. Crusoe <michael.crusoe at gmail.com> Mon, 16 Dec 2019 14:58:36 +0100
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Tue, 07 Jan 2020 14:24:53 +0100
libbio-cluster-perl (1.7.3-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -8,8 +8,8 @@ Build-Depends: debhelper-compat (= 12)
Build-Depends-Indep: perl,
libbio-perl-perl,
libxml-sax-perl,
- libtest-most-perl
-# libbio-variation-perl,
+ libtest-most-perl,
+ libbio-variation-perl
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/libbio-cluster-perl
Vcs-Git: https://salsa.debian.org/med-team/libbio-cluster-perl.git
@@ -19,7 +19,8 @@ Package: libbio-cluster-perl
Architecture: all
Depends: ${misc:Depends},
${perl:Depends},
- libbio-perl-perl
+ libbio-perl-perl,
+ libbio-variation-perl
Breaks: libbio-perl-perl (<< 1.7.3)
Replaces: libbio-perl-perl (<< 1.7.3)
Description: BioPerl cluster modules
=====================================
debian/patches/delete-bio-variation-parts deleted
=====================================
@@ -1,199 +0,0 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-Description: Bio::Variation::SNP is unmaintained and no longer released
-
-So remove references to it
---- libbio-cluster-perl.orig/lib/Bio/ClusterIO/dbsnp.pm
-+++ libbio-cluster-perl/lib/Bio/ClusterIO/dbsnp.pm
-@@ -65,7 +65,6 @@
- $Bio::ClusterIO::dbsnp::VERSION = '1.7.3';
- use strict;
- use Bio::Root::Root;
--use Bio::Variation::SNP;
- use XML::SAX;
- use Data::Dumper;
- use IO::File;
-@@ -167,108 +166,8 @@
- $DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0);
- }
-
--=head2 next_cluster
--
-- Title : next_cluster
-- Usage : $dbsnp = $stream->next_cluster()
-- Function: returns the next refSNP in the stream
-- Returns : Bio::Variation::SNP object representing composite refSNP
-- and its component subSNP(s).
-- Args : NONE
--
--=cut
--
--###
--#Adapted from Jason's blastxml.pm
--###
--
--# you shouldn't have to preparse this; the XML is well-formed and refers
--# accurately to a remote DTD/schema
--
--sub next_cluster {
-- my $self = shift;
-- my $data = '';
-- my($tfh);
--
-- if( $self->use_tempfile ) {
-- $tfh = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!");
-- $tfh->autoflush(1);
-- }
--
-- my $start = 1;
-- while( defined( $_ = $self->_readline ) ){
-- #skip to beginning of refSNP entry
-- if($_ !~ m{<Rs[^>]*>} && $start){
-- next;
-- } elsif($_ =~ m{<Rs[^>]*>} && $start){
-- $start = 0;
-- }
--
-- #slurp up the data
-- if( defined $tfh ) {
-- print $tfh $_;
-- } else {
-- $data .= $_;
-- }
--
-- #and stop at the end of the refSNP entry
-- last if $_ =~ m{</Rs>};
-- }
--
-- #if we didn't find a start tag
-- return if $start;
--
-- my %parser_args;
-- if( defined $tfh ) {
-- seek($tfh,0,0);
-- %parser_args = ('Source' => { 'ByteStream' => $tfh },
-- 'Handler' => $self);
-- } else {
-- %parser_args = ('Source' => { 'String' => $data },
-- 'Handler' => $self);
-- }
--
-- my $starttime;
-- my $result;
--
-- if( $DEBUG ) { $starttime = [ Time::HiRes::gettimeofday() ]; }
--
-- eval {
-- $result = $self->{'_xmlparser'}->parse(%parser_args);
-- };
--
-- if( $@ ) {
-- $self->warn("error in parsing a report:\n $@");
-- $result = undef;
-- }
--
-- if( $DEBUG ) {
-- $self->debug( sprintf("parsing took %f seconds\n", Time::HiRes::tv_interval($starttime)));
-- }
--
-- return $self->refsnp;
--}
--
- =head2 SAX methods
-
--=cut
--
--=head2 start_document
--
-- Title : start_document
-- Usage : $parser->start_document;
-- Function: SAX method to indicate starting to parse a new document.
-- Creates a Bio::Variation::SNP
-- Returns : none
-- Args : none
--
--=cut
--
--sub start_document{
-- my ($self) = @_;
-- $self->{refsnp} = Bio::Variation::SNP->new;
--}
--
- sub refsnp {
- return shift->{refsnp};
- }
---- libbio-cluster-perl.orig/META.json
-+++ libbio-cluster-perl/META.json
-@@ -46,7 +46,6 @@
- "Bio::Root::RootI" : "0",
- "Bio::Seq::SeqFactory" : "0",
- "Bio::Species" : "0",
-- "Bio::Variation::SNP" : "0",
- "Data::Dumper" : "0",
- "IO::File" : "0",
- "Time::HiRes" : "0",
---- libbio-cluster-perl.orig/META.yml
-+++ libbio-cluster-perl/META.yml
-@@ -39,7 +39,6 @@
- Bio::Root::RootI: '0'
- Bio::Seq::SeqFactory: '0'
- Bio::Species: '0'
-- Bio::Variation::SNP: '0'
- Data::Dumper: '0'
- IO::File: '0'
- Time::HiRes: '0'
---- libbio-cluster-perl.orig/Makefile.PL
-+++ libbio-cluster-perl/Makefile.PL
-@@ -30,7 +30,6 @@
- "Bio::Root::RootI" => 0,
- "Bio::Seq::SeqFactory" => 0,
- "Bio::Species" => 0,
-- "Bio::Variation::SNP" => 0,
- "Data::Dumper" => 0,
- "IO::File" => 0,
- "Time::HiRes" => 0,
-@@ -69,7 +68,6 @@
- "Bio::Root::Test" => 0,
- "Bio::Seq::SeqFactory" => 0,
- "Bio::Species" => 0,
-- "Bio::Variation::SNP" => 0,
- "Data::Dumper" => 0,
- "File::Spec" => 0,
- "IO::File" => 0,
---- libbio-cluster-perl.orig/t/ClusterIO.t
-+++ libbio-cluster-perl/t/ClusterIO.t
-@@ -7,7 +7,7 @@
- use lib '.';
- use Bio::Root::Test;
-
-- test_begin(-tests => 12,
-+ test_begin(-tests => 4,
- -requires_module => 'Time::HiRes');
-
- use_ok('Bio::ClusterIO');
-@@ -22,16 +22,16 @@
- '-format' => 'dbsnp',
- '-file' => test_input_file('LittleChrY.dbsnp.xml'));
-
-- $result = $clusterio->next_cluster;
-- ok($result);
-- is($result->observed, 'C/T');
-- is($result->type, 'notwithdrawn');
-- ok($result->seq_5);
-- ok($result->seq_3);
-- my @ss = $result->each_subsnp;
-- is scalar @ss, 5;
-- is($ss[0]->handle, 'CGAP-GAI');
-- is($ss[1]->handle, 'LEE');
-+ # $result = $clusterio->next_cluster;
-+ # ok($result);
-+ # is($result->observed, 'C/T');
-+ # is($result->type, 'notwithdrawn');
-+ # ok($result->seq_5);
-+ # ok($result->seq_3);
-+ # my @ss = $result->each_subsnp;
-+ # is scalar @ss, 5;
-+ # is($ss[0]->handle, 'CGAP-GAI');
-+ # is($ss[1]->handle, 'LEE');
-
- # don't know if these were ever meant to work... cjf 3/7/07
- #is($result->heterozygous, 0.208738461136818);
=====================================
debian/patches/series deleted
=====================================
@@ -1 +0,0 @@
-delete-bio-variation-parts
View it on GitLab: https://salsa.debian.org/med-team/libbio-cluster-perl/compare/1670917c83023699166aad85c8ab95be3f29c216...056967c79c4b1dc1136be5dfa5178799cd668563
--
View it on GitLab: https://salsa.debian.org/med-team/libbio-cluster-perl/compare/1670917c83023699166aad85c8ab95be3f29c216...056967c79c4b1dc1136be5dfa5178799cd668563
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