[med-svn] r12181 - in trunk/packages/gmod/gbrowse/trunk/debian: . patches

olivier sallou osallou-guest at alioth.debian.org
Fri Sep 7 09:43:13 UTC 2012 

Author: osallou-guest
Date: 2012-09-07 09:43:13 +0000 (Fri, 07 Sep 2012)
New Revision: 12181

Modified:
   trunk/packages/gmod/gbrowse/trunk/debian/changelog
   trunk/packages/gmod/gbrowse/trunk/debian/control
   trunk/packages/gmod/gbrowse/trunk/debian/get-orig-source
   trunk/packages/gmod/gbrowse/trunk/debian/patches/debian-packaging-patch
   trunk/packages/gmod/gbrowse/trunk/debian/patches/manpages.patch
   trunk/packages/gmod/gbrowse/trunk/debian/watch
Log:
prepare new upstream release

Modified: trunk/packages/gmod/gbrowse/trunk/debian/changelog
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/changelog	2012-09-06 20:30:44 UTC (rev 12180)
+++ trunk/packages/gmod/gbrowse/trunk/debian/changelog	2012-09-07 09:43:13 UTC (rev 12181)
@@ -1,7 +1,10 @@
-gbrowse (2.48~dfsg-2) UNRELEASED; urgency=low
+gbrowse (2.50+dfsg-1) UNRELEASED; urgency=low
 
   [ Olivier Sallou ]
   * NOT RELEASED YET
+  * New upstream release (Closes: #677381).
+  * Package VM::EC2 from CPAN is missing, need
+    to create a new package libvm-ec2-perl
 
   [ Andreas Tille ]
   * debian/upstream: Added citation information

Modified: trunk/packages/gmod/gbrowse/trunk/debian/control
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/control	2012-09-06 20:30:44 UTC (rev 12180)
+++ trunk/packages/gmod/gbrowse/trunk/debian/control	2012-09-07 09:43:13 UTC (rev 12181)
@@ -4,8 +4,10 @@
 Build-Depends: bioperl (>= 1.6.901), debhelper (>= 8),
  libbio-graphics-perl (>= 2.26), libcapture-tiny-perl, libcgi-session-perl (>= 4.02),
  libgd-gd2-perl (>= 2.07) | libgd-gd2-noxpm-perl (>= 2.07), libio-string-perl,
+ libtest-more-perl,
  libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl,
- perl (>= 5.10.0) | libextutils-cbuilder-perl, sqlite3,libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype (>=1.7), libjs-scriptaculous (>= 1.9)
+ perl (>= 5.10.0) | libextutils-cbuilder-perl, sqlite3,libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype (>=1.7), libjs-scriptaculous (>= 1.9),
+ libvm-ec2-perl
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Olivier Sallou <osallou at debian.org>,
  Charles Plessy <plessy at debian.org>, Aaron M. Ucko <ucko at debian.org>
@@ -22,7 +24,8 @@
  libcgi-session-perl (>= 4.02),
  libgd-gd2-noxpm-perl (>= 2.07) | libgd-gd2-perl (>= 2.07), libio-string-perl,
  libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl,
- perl (>= 5.10.0) | libextutils-cbuilder-perl, libterm-readkey-perl, sqlite3, libdbd-sqlite3-perl, libjs-prototype (>=1.7), libjs-scriptaculous (>=1.9)
+ perl (>= 5.10.0) | libextutils-cbuilder-perl, libterm-readkey-perl, sqlite3, libdbd-sqlite3-perl, libjs-prototype (>=1.7), libjs-scriptaculous (>=1.9),
+ libvm-ec2-perl
 Suggests: gbrowse-data, gbrowse-calign, libfile-nfslock-perl
 Description: GMOD Generic Genome Browser
  Generic Genome Browser is a simple but highly

Modified: trunk/packages/gmod/gbrowse/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/get-orig-source	2012-09-06 20:30:44 UTC (rev 12180)
+++ trunk/packages/gmod/gbrowse/trunk/debian/get-orig-source	2012-09-07 09:43:13 UTC (rev 12181)
@@ -15,9 +15,9 @@
 mv ../${UTAR} .
 tar -xzf ${UTAR}
 
-mv GBrowse-${VERSION} $PKG-${VERSION}~dfsg.orig # .orig is requested by Developers Reference 3.4.4 §6.7.8.2
+mv GBrowse-${VERSION} $PKG-${VERSION}+dfsg.orig # .orig is requested by Developers Reference 3.4.4 §6.7.8.2
 
-cd $PKG-${VERSION}~dfsg.orig
+cd $PKG-${VERSION}+dfsg.orig
 rm -rf contrib
 # Fix upstream bug 3321801
 chmod 644 t/testdata/conf/languages/POSIX.pm
@@ -26,5 +26,5 @@
 
 rm $UTAR
 
-BZIP2="--best" tar -cjf ${PKG}_${VERSION}~dfsg.orig.tar.bz2 ${PKG}-${VERSION}~dfsg.orig
-rm -rf ${PKG}-${VERSION}~dfsg.orig
+BZIP2="--best" tar -cjf ${PKG}_${VERSION}+dfsg.orig.tar.bz2 ${PKG}-${VERSION}+dfsg.orig
+rm -rf ${PKG}-${VERSION}+dfsg.orig

Modified: trunk/packages/gmod/gbrowse/trunk/debian/patches/debian-packaging-patch
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/patches/debian-packaging-patch	2012-09-06 20:30:44 UTC (rev 12180)
+++ trunk/packages/gmod/gbrowse/trunk/debian/patches/debian-packaging-patch	2012-09-07 09:43:13 UTC (rev 12181)
@@ -64,9 +64,9 @@
  check_all_files();
  check_data_sources();
 +}
+ fix_session_permissions();
  fix_sqlite_permissions() if $type =~ /sqlite/i;
  
- $database->disconnect;
 --- a/htdocs/index.html
 +++ b/htdocs/index.html
 @@ -24,7 +24,7 @@
@@ -110,7 +110,7 @@
    <li>FastCGI
 --- a/install_util/GBrowseInstall.pm
 +++ b/install_util/GBrowseInstall.pm
-@@ -32,6 +32,7 @@
+@@ -33,6 +33,7 @@
  		wwwuser       => 'User account under which Apache daemon runs?',
  		installconf   => 'Automatically update Apache config files to run GBrowse?',
  		installetc    => 'Automatically update system config files to run gbrowse-slave?',
@@ -118,7 +118,7 @@
      );
  my %OK_PROPS = @OK_PROPS;
  
-@@ -421,6 +422,83 @@
+@@ -422,6 +423,83 @@
  END
  }
  
@@ -202,7 +202,7 @@
  sub ACTION_install {
      my $self = shift;
      my $prefix = $self->install_base || $self->prefix || '';
-@@ -750,8 +828,9 @@
+@@ -773,8 +851,9 @@
  sub guess_user_account_db {
      my $self = shift;
      if (eval "require DBD::SQLite; 1") {

Modified: trunk/packages/gmod/gbrowse/trunk/debian/patches/manpages.patch
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/patches/manpages.patch	2012-09-06 20:30:44 UTC (rev 12180)
+++ trunk/packages/gmod/gbrowse/trunk/debian/patches/manpages.patch	2012-09-07 09:43:13 UTC (rev 12181)
@@ -62,7 +62,7 @@
  
 --- a/lib/Bio/Graphics/Browser2/DataBase.pm
 +++ b/lib/Bio/Graphics/Browser2/DataBase.pm
-@@ -63,12 +63,16 @@
+@@ -66,12 +66,16 @@
      $CACHE->delete($key);
  }
  
@@ -153,7 +153,7 @@
  The remainder of this document describes the methods available to the
 --- a/lib/Bio/Graphics/Browser2/DataSource.pm
 +++ b/lib/Bio/Graphics/Browser2/DataSource.pm
-@@ -31,6 +31,10 @@
+@@ -32,6 +32,10 @@
      }
  }
  
@@ -164,7 +164,7 @@
  =head1 SYNOPSIS
  
  =head1 DESCRIPTION
-@@ -149,6 +153,8 @@
+@@ -150,6 +154,8 @@
      delete $CONFIG_CACHE{$self->config_file};
  }
  
@@ -173,7 +173,7 @@
  =head2 userdata()
  
    $path = $source->userdata(@path_components)
-@@ -852,6 +858,8 @@
+@@ -855,6 +861,8 @@
    croak "Do not call make_link() on the DataSource. Call it on the Render object";
  }
  
@@ -182,7 +182,7 @@
  =item $db = $dsn->databases
  
  Return all named databases from [name:database] tracks.
-@@ -1086,6 +1094,8 @@
+@@ -1100,6 +1108,8 @@
      %DB_SETTINGS = ();
  }
  

Modified: trunk/packages/gmod/gbrowse/trunk/debian/watch
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/watch	2012-09-06 20:30:44 UTC (rev 12180)
+++ trunk/packages/gmod/gbrowse/trunk/debian/watch	2012-09-07 09:43:13 UTC (rev 12181)
@@ -1,3 +1,3 @@
 version=3
-opts=dversionmangle=s/~dfsg// \
+opts=dversionmangle=s/\+dfsg// \
 	http://search.cpan.org/dist/GBrowse .*/GBrowse-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)

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