[med-svn] r20825 - in trunk/packages/amap-align/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-12-19 08:22:37 +0000 (Sat, 19 Dec 2015)
New Revision: 20825

Added:
   trunk/packages/amap-align/trunk/debian/patches/mayhem.patch
Modified:
   trunk/packages/amap-align/trunk/debian/changelog
   trunk/packages/amap-align/trunk/debian/control
   trunk/packages/amap-align/trunk/debian/copyright
   trunk/packages/amap-align/trunk/debian/patches/series
Log:
Same fix as done for probalign - seems authors keep on ignoring getopt


Modified: trunk/packages/amap-align/trunk/debian/changelog
===================================================================
--- trunk/packages/amap-align/trunk/debian/changelog	2015-12-19 07:38:33 UTC (rev 20824)
+++ trunk/packages/amap-align/trunk/debian/changelog	2015-12-19 08:22:37 UTC (rev 20825)
@@ -1,9 +1,12 @@
-amap-align (2.2-5) UNRELEASED; urgency=medium
+amap-align (2.2-5) unstable; urgency=medium
 
   * Moved debian/upstream to debian/upstream/metadata
   * cme fix dpkg-control
+  * Fix Mayhem issue caused by not using getopt
+    Closes: #715630
+  * DEP5 fix
 
- -- Andreas Tille <tille at debian.org>  Sat, 19 Dec 2015 08:36:11 +0100
+ -- Andreas Tille <tille at debian.org>  Sat, 19 Dec 2015 09:17:45 +0100
 
 amap-align (2.2-4) unstable; urgency=low
 

Modified: trunk/packages/amap-align/trunk/debian/control
===================================================================
--- trunk/packages/amap-align/trunk/debian/control	2015-12-19 07:38:33 UTC (rev 20824)
+++ trunk/packages/amap-align/trunk/debian/control	2015-12-19 08:22:37 UTC (rev 20825)
@@ -8,7 +8,7 @@
 Standards-Version: 3.9.6
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/amap-align/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/amap-align/trunk/
-X-Homepage: http://bio.math.berkeley.edu/amap/ - upstream seems to be dead
+Homepage: http://code.google.com/p/amap-align/
 
 Package: amap-align
 Architecture: any

Modified: trunk/packages/amap-align/trunk/debian/copyright
===================================================================
--- trunk/packages/amap-align/trunk/debian/copyright	2015-12-19 07:38:33 UTC (rev 20824)
+++ trunk/packages/amap-align/trunk/debian/copyright	2015-12-19 08:22:37 UTC (rev 20825)
@@ -3,6 +3,10 @@
 Source: http://bio.math.berkeley.edu/amap/download
         This download area as well as the homepage vanished
 
+Files: *
+Copyright: 2005—2007 Ariel Schwartz <sariel at cs.berkeley.edu>
+License: PD
+
 Files: display/*
 Copyright: © 2007 Michael E. Smoot
 License: GPL-2+
@@ -23,11 +27,7 @@
  On Debian systems, the complete text of the GNU General Public
  License can be found in `/usr/share/common-licenses/GPL'.
 
-Files: *
-Copyright: 2005—2007 Ariel Schwartz <sariel at cs.berkeley.edu>
 License: PD
-
-License: PD
  The current version of AMAP uses the PROBCONS 1.09 code base for some of the
  input/output procedures, and for the calculation of posterior probabilities
  (see PROBCONS.README).

Added: trunk/packages/amap-align/trunk/debian/patches/mayhem.patch
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/mayhem.patch	                        (rev 0)
+++ trunk/packages/amap-align/trunk/debian/patches/mayhem.patch	2015-12-19 08:22:37 UTC (rev 20825)
@@ -0,0 +1,32 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 19 Dec 2015 08:36:11 +0100
+Bug-Debian: https://bugs.debian.org/715630
+Description: This patch is a bit non-C++-ish but I'm not a C++
+ programmer and considered this at least a solution and code that
+ ignores getopt does not deserve more care. :-(
+
+--- a/align/Amap.cc
++++ b/align/Amap.cc
+@@ -747,6 +747,7 @@ SafeVector<string> ParseParams (int argc
+   SafeVector<string> sequenceNames;
+   int tempInt;
+   float tempFloat;
++  int has_sequence_argument = 0;
+ 
+   for (int i = 1; i < argc; i++){
+     if (argv[i][0] == '-'){
+@@ -1049,9 +1050,14 @@ SafeVector<string> ParseParams (int argc
+       }
+     }
+     else {
++      has_sequence_argument = 1;
+       sequenceNames.push_back (string (argv[i]));
+     }
+   }
++  if (!has_sequence_argument) {
++    cerr << "ERROR: No MFAFILE specified" << endl;
++    exit(1);
++  }
+ 
+   if (enableTrainEmissions && !enableTraining){
+     cerr << "ERROR: Training emissions (-e) requires training (-t)" << endl;

Modified: trunk/packages/amap-align/trunk/debian/patches/series
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/series	2015-12-19 07:38:33 UTC (rev 20824)
+++ trunk/packages/amap-align/trunk/debian/patches/series	2015-12-19 08:22:37 UTC (rev 20825)
@@ -1,3 +1,4 @@
 fix-gcc-4.3.diff
 fix-gcc-4.6.diff
 hardening.patch
+mayhem.patch