[Pkg-emboss-commits] r89 - in emboss/tags/5.0.0-2/debian: . patches

Tue Jul 31 15:15:21 UTC 2007

Author: charles-guest
Date: 2007-07-31 15:15:21 +0000 (Tue, 31 Jul 2007)
New Revision: 89

Added:
   emboss/tags/5.0.0-2/debian/patches/psiphi-fix-2007-07-27.patch
Modified:
   emboss/tags/5.0.0-2/debian/changelog
   emboss/tags/5.0.0-2/debian/control
   emboss/tags/5.0.0-2/debian/patches/series
Log:
preparing the version 5.0.0-2, which diverges from the trunk

Modified: emboss/tags/5.0.0-2/debian/changelog
===================================================================

--- emboss/tags/5.0.0-2/debian/changelog	2007-07-31 15:09:31 UTC (rev 88)
+++ emboss/tags/5.0.0-2/debian/changelog	2007-07-31 15:15:21 UTC (rev 89)
@@ -2,11 +2,14 @@
 
   * Building the manpages offline to save buildd time, therefore not
     depending anymore on the XML toolchain.
-  * Gave their own packages to the AJAX and NUCL libraries.
-  * Removed the recommendation on dialign as edialign dissapeared.
-  * Removed the extra Tag field in debian/control.
+  * Using a emboss/psiphi.c file fixed by upstream
+    ftp://emboss.open-bio.org/pub/EMBOSS/fixes/psiphi.c
+  * Removed the recommendation on dialign, as edialign dissapeared.
+  * Thightened the Depends: relationship between emboss and
+    emboss-lib (Closes: #435232).
+  * Removed inactive developper from the uploaders list.
 
- -- Charles Plessy <charles-debian-nospam at plessy.org>  Fri, 27 Jul 2007 00:55:09 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Mon, 30 Jul 2007 23:22:11 +0900
 
 emboss (5.0.0-1) unstable; urgency=low
 

Modified: emboss/tags/5.0.0-2/debian/control
===================================================================
--- emboss/tags/5.0.0-2/debian/control	2007-07-31 15:09:31 UTC (rev 88)
+++ emboss/tags/5.0.0-2/debian/control	2007-07-31 15:15:21 UTC (rev 89)
@@ -2,7 +2,7 @@
 Section: science
 Priority: optional
 Maintainer: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
-Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>, Matt Hope <dopey at debian.org>, Nelson A. de Oliveira <naoliv at debian.org>
+Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>, Nelson A. de Oliveira <naoliv at debian.org>
 Build-Depends: debhelper (>= 5), quilt, libx11-dev, x-dev, libgdchart-gd2-xpm-dev, zlib1g-dev, libpng12-dev, libpcre3-dev
 XS-Vcs-Browser: http://svn.debian.org/wsvn/pkg-emboss/emboss/trunk/debian
 XS-Vcs-Svn: svn://svn.debian.org/svn/pkg-emboss/emboss/
@@ -10,7 +10,7 @@
 
 Package: emboss
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, emboss-data (= ${source:Version}), csh|c-shell
+Depends: ${shlibs:Depends}, ${misc:Depends}, emboss-lib (= ${source:Version}), emboss-data (= ${source:Version}), csh|c-shell
 Recommends: primer3
 Suggests: emboss-doc (= ${source:Version}), clustalw
 Description: The European Molecular Biology Open Software Suite
@@ -25,6 +25,7 @@
  commercial software packages.
  .
   Homepage: http://www.emboss.org
+XB-Tag: interface::commandline, scope::utility, field::biology, role::program
 
 Package: emboss-data
 Architecture: all
@@ -32,6 +33,7 @@
 Description: Data files for the EMBOSS package
  This package includes data files needed by EMBOSS, the European Molecular
  Biology Open Software Suite.
+XB-Tag: devel::runtime, field::biology, role::app-data
 
 Package: emboss-doc
 Section: doc
@@ -40,6 +42,7 @@
 Description: Documentation for EMBOSS
  This package includes non-essential user documentation for EMBOSS, the
  European Molecular Biology Open Software Suite.
+XB-Tag: made-of::data:postscript, field::biology, role::documentation
 
 Package: emboss-lib
 Section: libs
@@ -58,51 +61,4 @@
   * The NUCLEUS library provides higher-level functions specific to molecular
   sequence analysis, including sequence comparisons, translation, codon usage
   and annotation.
-
-Package: libajax-5.0.0
-Section: libs
-Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: Core library used by all EMBOSS applications.
-  This package contains a core library of the European Molecular Biology Open
-  Software Suite, EMBOSS.
-  .
-  AJAX covers standard data structures, including strings, sequences, file
-  handles, queues, hashes, heaps, lists, dictionaries, trees and dynamic
-  arrays. It also covers standard algorithms including comparisons, pattern
-  matching, sorting, and iterators. AJAX will also provide a set of high level
-  graphics functions suited to the needs of sequence analysis applications.
-  .
-  This package contains the runtime library files needed to run software
-  using libajax.
-
-Package: libajax-5.0.0-dev
-Section: libdevel
-Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: Development files for libajax
-  This package contains the header and development files needed to build
-  programs and packages using libajax.
-
-Package: libnucleus-5.0.0
-Section: libs
-Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: Core library used by all EMBOSS applications.
-  This package contains a core library of the European Molecular Biology Open
-  Software Suite, EMBOSS.
-  .
-  The NUCLEUS library provides higher-level functions specific to molecular
-  sequence analysis, including sequence comparisons, translation, codon usage
-  and annotation.
-  .
-  This package contains the runtime library files needed to run software
-  using libnucleus.
-
-Package: libnucleus-5.0.0-dev
-Section: libdevel
-Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: Development files for libajax
-  This package contains the header and development files needed to build
-  programs and packages using libnucleus.
+XB-Tag: field::biology, role::shared-lib

Added: emboss/tags/5.0.0-2/debian/patches/psiphi-fix-2007-07-27.patch
===================================================================
--- emboss/tags/5.0.0-2/debian/patches/psiphi-fix-2007-07-27.patch	                        (rev 0)
+++ emboss/tags/5.0.0-2/debian/patches/psiphi-fix-2007-07-27.patch	2007-07-31 15:15:21 UTC (rev 89)
@@ -0,0 +1,23 @@
+Index: EMBOSS-5.0.0/emboss/psiphi.c
+===================================================================
+--- EMBOSS-5.0.0.orig/emboss/psiphi.c
++++ EMBOSS-5.0.0/emboss/psiphi.c
+@@ -160,7 +160,7 @@
+     finishres = ajAcdGetInt("finishresiduenumber");
+ 
+     /* reserve memory for and read in structure */
+-    /* JISON */    pdb = ajPdbReadoldNew(pdbfile);
++    /* JISON */    pdb = ajPdbReadNew(pdbfile,0);
+     
+     /* check and set number of chain to be analysed */
+     highest = pdb->Nchn;
+@@ -440,6 +440,9 @@
+     ajint lowestres = 0;
+ 
+     AjPAtom inlist   = NULL;
++
++    if(!ajListGetLength(pdb->Chains[myindex]->Atoms))
++	ajFatal("Chain %d has no atoms",myindex+1);
+     
+     /* read first atom in list into memory, but keep it on list */
+     ajListPeek(pdb->Chains[myindex]->Atoms,

Modified: emboss/tags/5.0.0-2/debian/patches/series
===================================================================
--- emboss/tags/5.0.0-2/debian/patches/series	2007-07-31 15:09:31 UTC (rev 88)
+++ emboss/tags/5.0.0-2/debian/patches/series	2007-07-31 15:15:21 UTC (rev 89)
@@ -0,0 +1 @@
+psiphi-fix-2007-07-27.patch


