Lintian Fixes - massxpert

Ready changes

Merge these changes:

git pull https://janitor.debian.net/git/massxpert lintian-fixes/main

Summary

Diff

diff --git a/debian/changelog b/debian/changelog
index bb3ca516..2b413b03 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+massxpert (6.0.1-2) UNRELEASED; urgency=low
+
+  * Trim trailing whitespace.
+  * Use secure copyright file specification URI.
+
+ -- Debian Janitor <janitor@jelmer.uk>  Mon, 07 Sep 2020 09:09:35 -0000
+
 massxpert (6.0.1-1) unstable; urgency=low
 
   * Implement ready access to the user manual from the help/about dialog
@@ -15,8 +22,8 @@ massxpert (6.0.0-1) unstable; urgency=low
     so shipping it separately now makes sense.
 
   * Note that a number of deprecation warnings were fixed due to the
-    upgrade to Qt 5.14 from 5.12 (qSort() -> std::sort() and 
-    qGreater<Type>() -> std::greater<Type>() and 
+    upgrade to Qt 5.14 from 5.12 (qSort() -> std::sort() and
+    qGreater<Type>() -> std::greater<Type>() and
     QMatrix -> QTransform).
 
   * The version number starts at 6.0.0.
@@ -129,7 +136,7 @@ msxpertsuite (5.7.0-1) unstable; urgency=low
   * New upstream release featuring the ability to shape a mass peak centroid
     into a Gaussian/Lorentzian configurable peak. Update the user manual to
     document that new feature.
- 
+
   * Break msxpertsuite into two binary packages: msxpertsuite-massxpert and
     msxpertsuite-minexpert.
 
@@ -146,13 +153,13 @@ msxpertsuite (5.6.1-1) unstable; urgency=low
 msxpertsuite (5.6.0-1) unstable; urgency=low
 
   * New upstream version:
- 
+
     - Improve the interpreation of script lines;
     - Start implementation of a JavaScript script file to calibrate the Synapt
       data.
     - Improve the mass data integration in script mode;
     - When creating mass spectrum from clipboard, automatically trigger the
-      computation of the actual mass spectrum plot without requiring a TIC 
+      computation of the actual mass spectrum plot without requiring a TIC
       to mass spectrum computation.
     - Provide Savitzky-Golay filtering to any trace in any plot widget with
       undo/redo feature.
@@ -177,7 +184,7 @@ msxpertsuite (5.5.3-1) unstable; urgency=low
     triggers resolving power computation.
 
   * mineXpert: Make sure to test the ion mobility drift time as an xml string
-    value and not as a double value. 
+    value and not as a double value.
 
   * mineXpert: Make sure to craft an absolute path file name when exporting
     data in the SQLite3 db format.
@@ -206,21 +213,21 @@ msxpertsuite (5.5.0-1) UNRELEASED; urgency=low
   * New upstream release;
 
   * mineXpert: Add new figures to the user manual and replace others. Update the user manual;
-  
+
   * mineXpert: Provide a way for the user to configure the tolerance on the fractional part of the z value as is computed during deconvolution, document that new feature in the user manual;
-  
+
   * mineXpert: Ensure that the selection line, start and end markers and texts overlaid on the colormap are white-colored so that they can be visible on the dark blue background;
-  
+
   * mineXpert: Fix corner case crash when hitting Shift while right-button dragging in the colormap;
-  
+
   * mineXpert: Improve GUI in the data slicer window;
-  
+
   * mineXpert: When shift rescaling plots in multigraph plot widget, ensure the y axis full scale is determined on the basis of the greatest y value of all the graphs currently displayed in the view;
-  
+
   * mineXpert: Allow changing the color of a TIC chrom plot right after data file loading (that is, even if it has no relations to other plots);
-  
+
   * mineXpert: Replace ''TIC'' with ''XIC'' chromatogram text where needed;
-  
+
   * mineXpert: Add computation of resolving power when mouse is moved over spectrum.
 
  -- Filippo Rusconi <lopippo@debian.org>  Thu, 20 Sep 2018 15:44:55 +0200
@@ -452,7 +459,7 @@ msxpertsuite (3.8.1-1) unstable; urgency=low
 msxpertsuite (3.8.0-1) unstable; urgency=low
 
   * New upstream package:
-  
+
       * Major improvements to the scripting environment;
       * Major rewrite and increase of the mineXpert user manual section about
         scripting;
@@ -466,7 +473,7 @@ msxpertsuite (3.7.1-1) UNRELEASED; urgency=low
 
   * New classes to model simple Trace objects. MassSpectrum now derives from
     Trace. The most basic data object is now DataPoint, which replaces
-    MassPeak. 
+    MassPeak.
 
   * Added scriptability for DataPoint, Trace and MassSpectrum;
 
@@ -494,14 +501,14 @@ msxpertsuite (3.6.7-1) unstable; urgency=low
   * Replace devdoc/html/jquery.js by a symbolic link to the same file of the
     libjs-jquery package.
 
-  * Standards-Version: 4.0.1 
- 
+  * Standards-Version: 4.0.1
+
  -- Filippo Rusconi <lopippo@debian.org>  Mon, 11 Sep 2017 12:14:45 +0200
 
 msxpertsuite (3.6.6-1) unstable; urgency=low
 
-  * New upstream release. Mainly updated the dev docs and now 
-    building html doxygen-based documentation 
+  * New upstream release. Mainly updated the dev docs and now
+    building html doxygen-based documentation
     (binary package msxpertsuite-devdoc).
 
   * Occasional code cleanup and code improvements.
@@ -509,22 +516,22 @@ msxpertsuite (3.6.6-1) unstable; urgency=low
   * Make sure that the arch vs indep build is ok and does not depend on the
     order of building. Thanks again to Aaron M. Ucko  <ucko@debian.org> for
     reporting the building issue (Closes: 874530).
- 
+
  -- Filippo Rusconi <lopippo@debian.org>  Mon, 11 Sep 2017 10:07:25 +0200
 
 msxpertsuite (3.6.5-1) UNRELEASED; urgency=low
 
-  * New upstream release. Mainly updated the dev-docs and now 
-    building html doxygen-based documentation 
+  * New upstream release. Mainly updated the dev-docs and now
+    building html doxygen-based documentation
     (binary package msxpertsuite-devdoc).
- 
+
  -- Filippo Rusconi <lopippo@debian.org>  Tue, 05 Sep 2017 14:14:43 +0200
 
 msxpertsuite (3.6.4-1) unstable; urgency=low
 
   * New upstream release. Mainly updated the dev-docs that sit in the code
     (based on doxygen).
-  
+
   * CMake-based project build system improved to better separate the build of
     the "binary" components of the project from the build of the "indep"
     compoments of the project (see below for rationale).
@@ -599,7 +606,7 @@ massxpert (3.5.0-1) unstable; urgency=medium
 
   * moved upstream to upstream/metadata (Thanks Andreas Tille, although I
     had done this long ago, Mon Aug 18, without pushing, sadly).
-    
+
  -- Filippo Rusconi <lopippo@debian.org>  Wed, 01 Jul 2015 22:37:23 +0200
 
 massxpert (3.4.1-1) unstable; urgency=low
@@ -614,7 +621,7 @@ massxpert (3.4.1-1) unstable; urgency=low
   * debian/control: set debhelper dependency version to 9.20130630
   * massxpert.desktop: Icon=massxpert-icon-32 (no extension for filename)
   * massxpert.desktop: Categories=Science (one categ. only)
-  
+
  -- Filippo Rusconi <lopippo@debian.org>  Mon, 01 Jul 2013 14:25:27 +0200
 
 massxpert (3.4.0-2) UNRELEASED; urgency=medium
@@ -636,9 +643,9 @@ massxpert (3.4.0-1) unstable; urgency=low
     a multi-region selection or make a multi-selection region.
 
     - Refactored the mz lab GUI so as to greatly simplify its use.
-  
+
     - Update of the french translation.
-  
+
  -- Filippo Rusconi <lopippo@debian.org>  Tue, 25 Dec 2012 22:04:33 +0100
 
 massxpert (3.3.0-1) unstable; urgency=low
@@ -652,7 +659,7 @@ massxpert (3.2.4-1) unstable; urgency=low
 
   * debian/control: add Build-Depends: dpkg-dev (>= 1.16.1~) as lintian
     complained about transitive dependencies that should be made explicit.
-  
+
   * Added new modifications in the protein-1-letter chemistry definition.
 
  -- Filippo Rusconi <lopippo@debian.org>  Wed, 17 Oct 2012 20:37:47 +0200
@@ -662,7 +669,7 @@ massxpert (3.2.3-1) unstable; urgency=low
   * debian/rules: setting DPKG_EXPORT_BUILDFLAGS=1 to implement the Debian
     hardening guidelines.
 
-  * Modification in the dna.xml file to better document the photocleavable 
+  * Modification in the dna.xml file to better document the photocleavable
     biotin modification
 
  -- Filippo Rusconi <lopippo@debian.org>  Fri, 08 Jun 2012 11:09:47 +0200
@@ -681,9 +688,9 @@ massxpert (3.2.1-1) unstable; urgency=low
 
   * Upstream release:
 
-    - fix a bug in the definition of the protein chemical modifications 
+    - fix a bug in the definition of the protein chemical modifications
     TNB and  DTNB;
-  
+
   * Add debian/upstream to document a reference to a paper describing this
     software;
   * Fix problem with failing symbolic link between the massxpert and -dbg
@@ -704,8 +711,8 @@ massxpert (3.2.0-1) unstable; urgency=low
   * Upstream release:
 
     - Added feature to simulate fragmentations of oligomers that contain
-    cross-links. 
-    
+    cross-links.
+
     - Updated the user manual to document the new feature.
 
  -- Filippo Rusconi <lopippo@debian.org>  Sat, 22 Oct 2011 21:45:33 +0200
@@ -716,21 +723,21 @@ massxpert (3.1.0-1) unstable; urgency=low
 
     - Updated the user manual since a long time, documenting part of the
     features implemented since last manual update;
-  
+
     - Implemented automatic naming of XpertMiner input data dialog
     windows;
-  
+
     - Implemented export of XpertMiner output data into new input data
     dialog windows, so as to be able to chain calculations;
-    
+
     - Refactored isotopic cluster calculation code;
-    
+
     - Implemented a new spectrum calculation feature that simulates a
     complete spectrum starting from a list of oligomers obtained by
     cleavage of a polymer sequence. An isotopic cluster can be computed
     for each oligomer in the list or not. If not, the mono or avg mass can
     be used to compute the peak shape;
-    
+
     - Implemented a new spectrum calculation feature that simulates a
     complete spectrum starting from a list of analytes obtained by
     calculating a m/z ratio series with a elemental formula as the
@@ -741,7 +748,7 @@ massxpert (3.1.0-1) unstable; urgency=low
 massxpert (3.0.0-1) unstable; urgency=low
 
   * Upstream release:
-    
+
     - Major rework of the XpertMiner module;
     - Bug fixes;
     - Feature improvements.
@@ -751,14 +758,14 @@ massxpert (3.0.0-1) unstable; urgency=low
 massxpert (2.9.0-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - Switched to the TableView data display method the whole XpertMiner
     module. This allows for easier code maintaining and for clearer
     graphical user interface.
-    
+
     - Refactored code in the MzLabInputOligomerTreeView class code to
     improve quality and readability.
-  
+
     - Improved the XpertMiner window layout for more clarity.
 
     - Added feature to call a calculator window right from the sequence
@@ -769,7 +776,7 @@ massxpert (2.9.0-1) unstable; urgency=low
 massxpert (2.8.0-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - Switched to the TableView mass search oligomer display (was using
     TreeView);
 
@@ -778,10 +785,10 @@ massxpert (2.8.0-1) unstable; urgency=low
 massxpert (2.7.0-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - Switched to the TableView fragmentation oligomer display (was using
     TreeView);
-  
+
     - Added feature by which it is now possible to stack fragmentation
     oligomers from different fragmentation calculations, thus providing a
     way to have a single list of fragments calculated in different
@@ -792,7 +799,7 @@ massxpert (2.7.0-1) unstable; urgency=low
 massxpert (2.6.0-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - Completely refactored the code for the isotopic cluster
     simulator. Increased speed calculation by a factor ~8. In particular,
     the simulator now handles handsomely the heavily-charged large
@@ -804,10 +811,10 @@ massxpert (2.6.0-1) unstable; urgency=low
 massxpert (2.5.2-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - Fix regression causing a crash when fragmenting oligomers in any
     kind of situation. This fix is critical.
-  
+
  -- Filippo Rusconi <lopippo@debian.org>  Mon, 06 Jun 2011 02:34:46 +0200
 
 massxpert (2.5.1-1) unstable; urgency=low
@@ -815,16 +822,16 @@ massxpert (2.5.1-1) unstable; urgency=low
   * Modified the email address of the uploader to my debian address
     lopippo@debian.org.
   * Removed the DM-Upload-Allowed bit.
-  
+
   * New upstream release:
-  
+
     - Fix serious bug that crashed the program upon recleaving a polymer
     within the same CleavageDlg window. That bug appeared related to the
     upgrade of the Qt libraries as it crept without modifications of the
     massXpert source code. The cleavage oligomers are now displayed in a
     QTableView widget instead of a QTreeView widget which simplified a lot
     both the code and the graphics display of the data.
-  
+
     - Fix problems with the reliability of the cleavage details that were
     provided as feedback when an oligomer from the tree/table view was
     selected.
@@ -834,7 +841,7 @@ massxpert (2.5.1-1) unstable; urgency=low
 massxpert (2.5.0-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - Implement feature allowing one to apply formulas commonly found
     during fragmentation, like loss of water or loss of ammonia, to each
     fragment oligomer computed for any given fragmentation pattern.
@@ -844,7 +851,7 @@ massxpert (2.5.0-1) unstable; urgency=low
 massxpert (2.4.4-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - Fix FTBFS with gcc-4.6 -Werror (this package builds with -Werror,
     and GCC 4.6 triggers new warnings) reported by Matthias Klose
     <doko@debian.org> (Closes: #625382).
@@ -853,27 +860,27 @@ massxpert (2.4.4-1) unstable; urgency=low
 
 massxpert (2.4.3-1) unstable; urgency=low
 
-  * Upstream release. 
-    
+  * Upstream release.
+
     - Rewrote the Formula's elementalComposition() so that the order of
     the atoms is in the CHNO->alphabetic conventional order;
-    
+
     - Added ion charge proton to the formula of the z fragmentation
     specification;
-    
+
     - Added feature: when running the mz calculations dialog from the
     sequence editor window, the masses are automatically set in the dialog
     window
-    
+
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Sat, 19 Feb 2011 19:11:35 +0100
 
 massxpert (2.4.2-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - Fix bug (Closes: #611142) due to insufficient checking of the array
     boundary upon clicking on the sequence editor outside of the vignettes.
-  
+
     - debian/control : Standards-Version: 3.9.1.
 
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Tue, 25 Jan 2011 23:26:23 +0100
@@ -890,16 +897,16 @@ massxpert (2.4.1-1) unstable; urgency=low
 massxpert (2.4.0-1) unstable; urgency=low
 
   * Upstream release:
-  
+
     - Monoisotopic mass is now the mass of the isotope of highest
     abundance and not of lowest mass. This won't change anything for
     biopolymers, as all the chemical elements used there have their
     lightest isotope of highest abundance;
 
     - Update the french translation;
-    
+
     - Add two peptide example files.
-  
+
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Fri, 10 Dec 2010 11:16:30 +0100
 
 massxpert (2.3.6-1) unstable; urgency=low
@@ -910,35 +917,35 @@ massxpert (2.3.6-1) unstable; urgency=low
     not encompassing all the cross-linked monomers;
 
     - Fix a linker flag for the MacOSX PPC build;
-    
+
     - Fix a GUI bug in the sequence editor window
     (gui/monomerCodeEvaluator.cpp).
-  
+
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Mon, 10 May 2010 20:16:34 +0200
 
 massxpert (2.3.5-1) unstable; urgency=low
 
   * Upstream release:
-    
+
     - Add feature to compute the mass differences between any two monomers
     in the polymer chemistry definition;
-    
+
     - Update the user manual to document the new feature.
 
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Thu, 29 Apr 2010 15:13:50 +0200
 
 massxpert (2.3.0-1) unstable; urgency=low
 
-  * Upstream release: 
-    
+  * Upstream release:
+
     - Add feature to allow cleaving polymer sequences only in the
     currently selected region of the sequence;
-    
+
     - Improvements in the GUI of the cleavage dialog window;
-    
+
     - Fix one bug in the constructor of the CalcOptions object, which
     failed to correctly initialize the CoordinateList member data;
-    
+
     - Update the documentation (user manual) to describe the new cleavage
     feature.
 
@@ -947,22 +954,22 @@ massxpert (2.3.0-1) unstable; urgency=low
 massxpert (2.2.0-1) unstable; urgency=low
 
   * Upstream release:
-  
+
     - Fix bug with polymer sequence not saving a modified name in the
     sequence editor window;
-  
+
     - Implemented a protein sequence importer for PDB cristallographic
     data;
-    
+
     - Update the french translation;
-  
+
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Tue, 20 Apr 2010 22:37:24 +0200
 
 massxpert (2.1.1-1) unstable; urgency=low
 
   * Upstream release:
     - Fix programming error: use of an uninitialised variable.
-  
+
   * debian/rules: remove the 'dh_desktop -a' call.
 
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Wed, 13 Jan 2010 20:49:30 +0100
@@ -970,17 +977,17 @@ massxpert (2.1.1-1) unstable; urgency=low
 massxpert (2.1.0-1) unstable; urgency=low
 
   * Upstream release:
-    
+
     - Show the current selection coordinates in the sequence editor window;
-    
+
     - Fixed nasty bug due to reusing freed memory. Interestingly, that bug
     only showed up on MOSX;
-    
+
     - Code cleanup (amongs which a number of C-style casts were moved to
       C++-reinterpret_cast's;
-      
+
     - Fix memory leaks;
-  
+
     - Fix programming style glitches.
 
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Tue, 22 Dec 2009 15:44:58 +0100
@@ -988,138 +995,138 @@ massxpert (2.1.0-1) unstable; urgency=low
 massxpert (2.0.9-1) unstable; urgency=low
 
   * Upstream release:
-    
+
     - Fixed a bug causing a crash in corner polymer cleavage cases.
 
   * Switched to source format 3.0 (quilt);
-  
+
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Thu, 26 Nov 2009 20:51:48 +0100
 
 massxpert (2.0.8-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - data : fix dna polymer chemistry definition to include
     phosphorothioates;
-  
+
     - Added feature to regularly recall to the user to cite massXpert in
     the About dialog window;
-    
+
     - data: ix monomer definition for uracile;
-    
+
     - New version of the massxpert.spec taken from Thomas Spura
     <tomspur@fedoraproject.org>
-    
+
     - data: added deuterium to atom definitions;
-    
+
     - Enable installing the plugins in a specific directory (to help with
     distributions willing to put shared binaries in /usr/lib64);
-    
+
     - XpertMiner : fix potentially massive memory leaks. Thanks cppcheck;
-  
+
     - Code documentation and cleanup;
-    
+
     - XpertCalc: formulas that were added to the memory of the calculator
     can now be removed;
-    
+
     - XpertCalc : implemented per polymer chemistry definition handling of
     window geometry settings;
-    
+
     - data: mprove fragmentation definitions for dna;
-    
+
     - Fix bug due to not really checking the formula syntax while it was
     reported as validated;
-    
+
     - Formulas now accept a double-quote-enclosed title and spaces.
-    
+
   * debian/copyright: add blurb about location of the GPL-3 license on
     Debian systems.
-  
-  
+
+
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Sat, 21 Nov 2009 20:04:21 +0100
 
 massxpert (2.0.7-1) unstable; urgency=low
 
   * New upstream release:
-  
+
   * Fix problem with version numbering in the previous release;
-  
+
   * Fix absence of the corresponding .orig.tar.gz (made erroneously a
     native package).
 
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Mon, 05 Oct 2009 22:54:42 +0200
- 
-  
+
+
 massxpert (2.0.6.-1) unstable; urgency=low
-  
+
   * Upstream release:
-  
+
     - Fixes to nroff formatting of the man pages (thanks to Daniel Leidert
     for suggestions);
 
     - XpertCalc: added possibility to insert formulas in the formula line
     edit by Ctrl-clicking buttons in the chemical keypad;
-  
+
     - XpertCalc: added possibility to surround formulas with spaces for
     much better readability in case of complex structures. This is
     performed by Shit-Ctrl-cliking on the chemical pad buttons;
 
     - XpertCalc: automatically seed m/z calculation dialog window with
     masses from the XpertCalc main window;
-    
+
     - XpertEdit: bug fix in the sequence editor's feedback to the user
     upon entering a bad monomer code character. When a new valid character
     is entered this old error message is removed;
-  
+
     - XpertCalc: added lots of useful buttons to the dna chemical pad
     configuration file;
-    
+
     - Added bibliographical reference to the massXpert paper in
     _Bioinformatics_ to the man pages;
-    
+
     - XpertCalc: added possibility to store formula in a drop-down list so
     as to be able to recall them in ulterior calculations;
-    
+
     - XpertCalc: implemented new feature by which it is possible to set a
     title to a formula like the following : "initial-dimer" C5H6O9P3,
     which will be interpreted as formula "C5H6O9P3".
-    
+
     - Sequence editing plugins: added possibility to perform more
     sophisticated translation, like from codon to 1-letter code or from
     codon to 3-letters code (protein chemistry);
-    
+
     - XpertEdit: the tool box (available monomers/mass calculation engine
     configuration) now saves its position;
-    
+
     - Improved the CMake-based build system to automatically build the
     binary and the data if nothing is specified on the configuration
     command line (usermanual is not built by default; thanks to Pere
     Constans for reporting);
-    
+
     - Bunch of code tidying and memory leaks fixing (thanks to cppcheck,
     as suggested by Pere Constans);
-    
+
     - XpertEdit: fixed wrong behaviour in the whole/selected sequence
     logic in the mass search dialog window;
-    
+
     - XpertEdit: fixed the multi-character code disambiguation mechanism
     in the sequence editor's available codes tool box widget: it's
     triggered by hitting Ctrl-Enter;
-    
+
     - Xpertedit/XpertDef: improved feedback to the user on file save
     operation errors;
-    
+
     - XpertEdit/XpertDef: added possibility to show non-*.mxp/non-*.xml
     files in the openfile dialogs;
-    
+
     - XpertEdit: improved fragmentation with multiply-charged fragments:
     When there are multiply-charged fragments, the mass now takes into
     account the ionization rule that sits in the sequence editor windows's
     calculation engine configuration.
-    
+
     - Added Doxygen configuration file. Docs generated outside of the
     source tree.
-    
+
     - XpertEdit: fix bug in elementalComposition() that would fail when
     count is negative.  Added simplify() function that calls
     elementalComposition() in turn.  Also fixed the way atomCount objects
@@ -1128,15 +1135,15 @@ massxpert (2.0.6.-1) unstable; urgency=low
 
     - XpertCalc: added possibility to simplify a complex set of formulas
     into a single factorized formula.
-    
-  
+
+
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Mon, 05 Oct 2009 10:55:32 +0200
 
 
 massxpert (2.0.5-1) unstable; urgency=low
 
   * Upstream release:
-  
+
     - Bug fix release : one serious bug was fixed, whereby the program
     would crash upon re-cleaving a polymer sequence in the same cleavage
     dialog window. This bug was already present (and silent) in previous
@@ -1148,32 +1155,32 @@ massxpert (2.0.5-1) unstable; urgency=low
 
 
 massxpert (2.0.4-1) unstable; urgency=low
-  
+
   * Upstream release:
-  
+
     - Performed an extensive cleaning work on the messages to the user and
     in the GUI messages. Updated the french translation accordingly. Fixes
     in the GUI stuff itself (like setting line edit widgets to read-only
     where necessary);
-  
+
     - XpertCalc: allow pasting the chempad's button's formula in the
     formula line edit widget instead of immediately accounting it in the
     results masses;
-  
+
     - XpertCalc: remove spaces from the formula entered in the calculator
     window;
-    
+
     - XpertCalc: rework the chemical pad specification to allow grouping
     of buttons and their coloring along with coloring of the group boxes;
-  
+
     - XpertCalc: update all the chemical pad configuration files of the
     distribution to the new format (chem_pad.conf files);
-  
+
     - User manual: update to document the new features of the calculator;
-  
+
     - XpertCalc: fixed a bug due to not really clearing seed/result masses
     when later using the chemical pad;
-  
+
   * massxpert.1 man page: specify better the location of the GPL-3 file on
     Debian systems.
 
@@ -1182,105 +1189,105 @@ massxpert (2.0.4-1) unstable; urgency=low
   * debian/rules: remove the CFLAGS = -Wall -g setting as it is already set.
 
   * debian/rules: change CFLAGS to CXXFLAGS.
-	
+
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Tue, 01 Sep 2009 15:45:56 +0200
 
-  
+
 massxpert (2.0.3-1) unstable; urgency=low
 
   * debian/control: Rename binary package from massxpert-bin to massxpert
     and remove Section: science field (inherits from the source package);
-  
+
   * debian/control: Move all the Build-Depends-Indep dependencies
     (texlive-latex-recommended,qtexlive-fonts-recommended) to
     Build-Depends dependencies (Closes: #528086) to work around the
     builders bug. For more details, see bugs:
-  
+
     - Bug #528086: massxpert_2.0.0-1(mips/unstable): FTBFS:
     missing build dependency
-    
-    - Bug #521918: pbuilder --build --binary-arch invokes 'build' target. 
-  
+
+    - Bug #521918: pbuilder --build --binary-arch invokes 'build' target.
+
   * debian/control: Remove no more required Build-Depends-Indep
     latex-related cm-super-minimal package (thanks to removing
     dependencies in the UseLATEX.cmake file;
-  
+
   * debian/control: Add Vcs-Git and Vcs-Browser fields;
-  
+
   * debian/control: Set Uploaders to Filippo Rusconi
     <rusconi-debian@laposte.net>;
-  
+
   * debian/control: Set Maintainer to The Debichem Group
     <debichem-devel@lists.alioth.debian.org>;
-  
+
   * debian/rules: Remove old unused variables;
-  
+
   * debian/rules: Fully separated the arch/indep targets which build and
     install stuff in different directories;
-  
+
   * debian/rules: .PHONY targets are now individually specified (so as not
     to forget them when targets change);
-  
+
   * debian/control: remove unrequired Build-Depends-Indep packages;
 
   * debian/watch: added file;
-    
+
   * debian/control: massxpert-bin to massxpert renaming:
     Conflict/Replace massxpert-bin
-	
+
   * New upstream release (worked a lot with Lionel Elie Mamane):
-    
+
     - gui/massxpert_fr.ts: updated the french translation;
-    
+
     - usermanual/front-matter.tex & usermanual/massxpert.tex: remove user
     manual dependency on LaTeX package "textcomp", so as not to embed
     Type3 fonts in the PDF file. Replaced (C) with \copyright. Small
     typographical fixes.
-    
+
     - usermanual/UseLATEX.cmake: remove other non-essential software
     requirements to reduce dependencies;
-    
+
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Wed, 10 Jun 2009 14:33:04 +0200
 
 massxpert (2.0.2-1) UNRELEASED; urgency=low
 
   * New upstream release (worked a lot with Lionel Elie Mamane):
-    
+
     - usermanual/CMakeLists.txt: remove the "-Werror" flag as almost any
     LaTeX compilation produces warnings;
-    
+
     - gui/application.cpp: set sensible values for the default decimal
     places to use to display numerical data on the first program run;
-    
+
     - usermanual/UseLATEX.cmake: update Copyright notice to reflect the
     fact that the file was modified by me;
     - lib/configSettings.cpp: remove unncessary configuration settings
     feedback messages, other improvements;
-  
+
     - gui/main.cpp: remove unnecessary feedback for the loading of
     translation files;
-  
+
     - Added 'Close' button to aboutDlg dialog window.
-    
+
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Fri, 15 May 2009 18:00:22 +0200
 
 massxpert (2.0.1-1) UNRELEASED; urgency=low
-  
+
   * New upstream release: bug fix release and other improvements.
-  
+
     - Clean source tree;
-    
+
     - lib/configSettings.cpp: fix typo (thanks Lionel Mamane);
-    
+
     - Modify usermanual build process to use UseLATEX.cmake;
-    
+
     - Fix bug due to not taking into account the locale while making
     textual mass lists starting from oligomer items in treeviews.
-    
+
     - Fix locale-specific input/output inconsistencies;
-    
+
     - Improved the simulations' result export as text;
-    
+
     - usermanual/UseLATEX.cmake: removed the requirement of
     /usr/bin/convert from ImageMagick as we do not need it: using pdflatex
     and only png-format graphics files;
@@ -1288,39 +1295,39 @@ massxpert (2.0.1-1) UNRELEASED; urgency=low
  -- Filippo Rusconi <rusconi-debian@laposte.net>  Wed, 15 Apr 2009 21:17:17 +0200
 
 massxpert (2.0.0-1) unstable; urgency=low
-  
+
   * Standards version is 3.8.1.
 
   * Bumped debian/compat to 7.
-  
+
   * Entirely reworked debian/rules, which now has build-arch and
     build-indep fully separated targets totally fitting the Build-Depends
     and Build-Depends-Indep fields of debian/control.
-  
+
   * New upstream release:
-  
+
     - Fixed bug in XpertDef due to not verifying upon removal of a
     modification if it is used by a cross-linker. Crashes. Report by Ron
     Bakus (UCSD domain edu).
 
     - Fixed bug with storing polymer sequences and polymer chemistry
     definitions with crippled XML;
-  
+
     - Added configurability to the number of decimal places used to
     display values for pH/pKa, atoms/isotopes, oligomers, polymers;
-  
+
     - Fixed regression with un-cross-linking;
-  
+
     - Fixed bug with calculation of right-end fragment boundaries;
-  
+
     - Big work within the XpertMiner module;
-  
+
     - Huge internal work with the ionization paradigm in particular within
     the fragmentation framework.
 
   * Fixes with the debian/* so that the source package now build three
     packages: massxpert-bin, massxpert-data, massxpert-doc.
-  
+
   * A bunch of improvements in the Debian packaging thanks to Lionel
     Mamane mentoring (parallel support in rules and others).
 
@@ -1331,9 +1338,9 @@ massxpert (2.0.0-1) unstable; urgency=low
 massxpert (1.7.8-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - Implemented multi-cleavages;
-  
+
     - Updated the User Manual
 
  -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Tue, 08 Jul 2008 13:09:31 +0200
@@ -1341,7 +1348,7 @@ massxpert (1.7.8-1) unstable; urgency=low
 massxpert (1.7.7-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - Implemented multi-region selections;
 
     - Updated the User Manual.
@@ -1351,19 +1358,19 @@ massxpert (1.7.7-1) unstable; urgency=low
 massxpert (1.7.6-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - Moved the project to GNU GPL version 3;
-  
+
     - Fixes for GUI bugs;
-  
+
     - Fixes with the localization of double values in the GUI;
-  
+
     - First implementation of the mzLab (still experimental feature);
-  
+
     - Classes rework with better handling of ionization throughout the whole project;
-  
+
     - Code cleanup, better handling of constness in the whole project;
-  
+
     - Updated the User Manual.
 
  -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Wed, 28 May 2008 15:18:37 +0200
@@ -1371,14 +1378,14 @@ massxpert (1.7.6-1) unstable; urgency=low
 massxpert (1.7.5-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - Code cleanup throughout the code redesign of some classes and addition
     of Ion class;
-  
+
     - Implemented namespace massXpert throughout the project;
-  
+
     - Update of the french translation;
-  
+
     - Bug fixes;
 
  -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Thu, 24 Apr 2008 21:12:56 +0200
@@ -1386,12 +1393,12 @@ massxpert (1.7.5-1) unstable; urgency=low
 massxpert (1.7.4-1) unstable; urgency=low
 
   * New upstream release:
-  
+
     - Implemented new means to define fragmentation specifications that
     involve the decomposition of the fragmented monomer's side chain;
-  
+
     - Fixed memory leak and bugs;
-  
+
     - Updated the french translation and the user manual.
 
  -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Wed, 02 Apr 2008 22:59:50 +0200
@@ -1401,16 +1408,16 @@ massxpert (1.7.3-1) unstable; urgency=low
   * Upstream release with main new feature: the filtering implemented for
     the previous version was extended also for the fragmentation and mass
     searching oligomer data;
-  
+
   * Improved the use of the filtering feature thanks to modifications in
     the graphical user interface;
-  
+
   * Implemented check that a cross-link name cannot be used already as a
     modification name (and vice versa);
-  
+
   * Fixes to regressions that crept in during last version developments
     and code cleanup;
-  
+
   * Update of the documentation;
 
  -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Sun, 30 Mar 2008 17:34:27 +0200
@@ -1420,9 +1427,9 @@ massxpert (1.7.2-1) unstable; urgency=low
   * Upstream release with main new figure: the oligomer data from a
     polymer sequence cleavage might be filtered live and in-place using a
     sortingProxy treeview (powerful feature of the Qt library);
-  
+
   * User manual update;
-  
+
   * Minor bugfixes.
 
  -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Tue, 25 Mar 2008 22:11:17 +0100
@@ -1430,7 +1437,7 @@ massxpert (1.7.2-1) unstable; urgency=low
 massxpert (1.7.1-1) unstable; urgency=low
 
   * Upstream release with main new feature: intra-molecular cross-links.
-  
+
   * Bug fixes and small improvements here and there.
 
   * Modified dh_shlibs line to exclude the plugins from the scan, as these
@@ -1440,18 +1447,18 @@ massxpert (1.7.1-1) unstable; urgency=low
 
 massxpert (1.7.0-1) unstable; urgency=low
 
-  * Upstream bug-fix release. 
-  
+  * Upstream bug-fix release.
+
   * Fixed crash caused by elemental compositions calculations using
     manually-defined polymer sequence modifications (thanks to as
     calculations session with Fatima Boutimah in my lab);
-  
+
   * Modified the polymer sequence file format so as to be able to save
     polymer sequence modifications with a fully qualified <mdf> (see
     polChemDef format) element. This allows storing the modifications with
     full qualification (and not only name) even when the modification is
     manually-defined.
-  
+
   * Added man massxpert-doc.7 page documenting the User manual.
 
  -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Thu, 21 Feb 2008 14:28:55 +0100
@@ -1460,9 +1467,9 @@ massxpert (1.6.9-1) unstable; urgency=low
 
   * Upstream release with more flexible monomer modification procedure
     (big inner code changes not visible by the user).
-  
+
   * Update the documentation.
-  
+
   * Extended copyright to 2008.
 
  -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Fri, 15 Feb 2008 10:48:49 +0100
@@ -1491,38 +1498,38 @@ massxpert (1.6.8-1) unstable; urgency=low
 massxpert (1.6.7-1) unstable; urgency=low
 
   * Upstream release with the following modifications:
-  
+
   * CMake'ization of the source tree.
-  
+
   * Fixed bug with calculation net charges with any given pH.
-  
+
   * Standards-Version: 3.7.2
 
  -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Sun, 09 Dec 2007 18:40:55 +0100
 
 massxpert (1.6.6-1) unstable; urgency=low
 
-  * Upstream release with the following modifications: 
-  
-  * Update the french translation and the user manual to reflect the 
+  * Upstream release with the following modifications:
+
+  * Update the french translation and the user manual to reflect the
     new features of the cleavage- and fragmentation-base oligomer
     generation.
-  
+
   * The oligomers from cleavage and fragmentation might now be calculated
     as multi-charged oligomers
-  
+
   * Implemented the fragmentation stuff in new class MxpFragmenter and
     removed the corresponding code from the fragmentation dialog
     class. Also, made the same use of QList<MxpOligomerList *> * instead
     of two nested QList objects as previously performed with the cleavage
     code in the fragmentation code.
-    
+
   * Implemented ionization level ranges for oligomers, starting with the
     cleavage application bits
   * Reimplemented the gui polymer sequence cleaving stuff to use the
     modified MxpCleaver object
   * Reimplemented the cleaver object to use the new oligomer list object
-  
+
   * Implemented and added to library 'list of oligomers' new class:
     MxpOligomerList derived from QList<MxpOligomer *>
 
@@ -1530,29 +1537,29 @@ massxpert (1.6.6-1) unstable; urgency=low
 
 massxpert (1.6.5-1) unstable; urgency=low
 
-  * Upstream release with the following modifications: 
-  
+  * Upstream release with the following modifications:
+
   * Added possibiliy to restrict monomer modifications to given
     monomers. If the user tries to modify a monomer with a modification
     that is not supported for it, the modification does not occur and the
     user gets a message. Implemented a mechanism by which these monomer
     modification limitations can be overridden.
-  
+
   * Fixed bug with parsing atom symbols with more than 2 characters.
-  
+
   * Added fake atoms so as to to allow defining formulas with precise
     masses.
-  
+
   * Fixed bug with creation of default monomer modification vignette and
     setting it to the hash with a bad key. That would lead to bad
     reference counting and crashes upon unmodification of more than one
     modified monomer.
-  
+
   * Better feedback messages to the sequence editor window's statusBar
     while doing initial sequence drawing.
-  
+
   * Updated french translation.
-  
+
   * Reverted to version 2 of the GPL as the Qt libraries are not using the
     'version 2 or any later version' wording.
 
@@ -1561,7 +1568,7 @@ massxpert (1.6.5-1) unstable; urgency=low
 massxpert (1.6.4-1) unstable; urgency=low
 
   * Upstream release with the following modifications:
-  
+
   * Translated the application into french. Took advantage of the
   translation work to uniformize the messages and the labels on the UI
   widgets.
@@ -1583,22 +1590,22 @@ massxpert (1.6.4-1) unstable; urgency=low
 massxpert (1.6.3-1) unstable; urgency=low
 
   * New upstream release.
-  
-  * Fixed glitches in some fields of the debian/control file.	
+
+  * Fixed glitches in some fields of the debian/control file.
 
   * Fixed problems with the modification vignettes and declarations of
     modifications in the modification_dictionary of some polymer
     chemistry definition.
 
-  * Many improvements in the user manual. 
-  
-  * Improved handling of polymer sequence modifications. 
-  
-  * Improvements the GUI and in the calculator recorder output. 
+  * Many improvements in the user manual.
+
+  * Improved handling of polymer sequence modifications.
+
+  * Improvements the GUI and in the calculator recorder output.
 
   * Added possibility to modify a polymer sequence arbitrarily by
   entering a chemical formula and not by choosing a modification in
-  the polymer chemistry definition. 
+  the polymer chemistry definition.
 
   * Switch to 4.3.0 as the Qt dependency, which showed some glitches
   in the handling of the sequence editor graphics view that were
@@ -1618,4 +1625,3 @@ massxpert (1.6.0-rc2-1) unstable; urgency=low
   * Initial release.
 
  -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Sun,  1 Jul 2007 18:49:17 +0200
-
diff --git a/debian/copyright b/debian/copyright
index 08c192ed..2416c970 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -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/
 Upstream-Name: massxpert
 Source: http://www.msxpertsuite.org
 

Debdiff

[The following lists of changes regard files as different if they have different names, permissions or owners.]

Files in second set of .debs but not in first

-rw-r--r--  root/root   /usr/lib/debug/.build-id/73/5a9a63cb3e4a717e8ef8fe9dc05efa5ba33a65.debug

Files in first set of .debs but not in second

-rw-r--r--  root/root   /usr/lib/debug/.build-id/6a/b65e6a907a7ded0d513ea53d2fb4539131ae30.debug

No differences were encountered between the control files of package massxpert

No differences were encountered between the control files of package massxpert-data

Control files of package massxpert-dbgsym: lines which differ (wdiff format)

  • Build-Ids: 6ab65e6a907a7ded0d513ea53d2fb4539131ae30 735a9a63cb3e4a717e8ef8fe9dc05efa5ba33a65

No differences were encountered between the control files of package massxpert-doc

Run locally

Try this locally (using the lintian-brush package):

debcheckout massxpert
cd massxpert
lintian-brush

More details

Full run details